There are several possibilities here, although generally they all have the same solution.
The English is poor or incorrect and the company did not check it well
It is possible that the company that checked your article did a bad job. This happens. Maybe the service did not have a native English speaker check your article. Maybe they had a bad day. Maybe they don't provide good service, and you just got lucky on previous times. It's hard to say.
The English is grammatical, but not idiomatic
It is possible that the company that checked your article fixed all the grammatical mistakes, but that there are still some phrasings which are not idiomatic or particularly natural. This is essentially a function of how detailed the corrections were. For example, here is the first paragraph of your post:
Recently I had submitted a Manuscript to an International Journal. Though it is accepted as a Minor revision, but I am worried about the reviewer's comment. First reviewer has commented that the Paper is well written, still needs some English improvements. Second reviewer has also commented that English improvements is required.
There are some small grammatical errors, and I can correct them as follows (in bold):
Recently I had submitted a manuscript to an international journal. Though it
is was accepted as a minor revision, but I am worried about the reviewer's comment. The first reviewer has commented that the paper is well written, but still needs some English improvements. The second reviewer has also commented that English improvements is are required.
While this paragraph is now grammatically correct, it still does not feel like it was written by a native speaker, and the way some words are used is a little odd. (E.g. using though and but in the second sentence; you really only need one of them.) So, a more thorough checking would suggest edits like the following:
had submitted a manuscript to an international journal. Though it is was accepted as a Minor revision pending minor revisions, but I am worried about the reviewers' s comments. The first reviewer has commented that the paper is well written, but still needs some English improvements. The second reviewer has also commented that English improvements is are required.
The checking service could have done the first step (making it grammatically correct) without following through on the second step (making it idiomatic). The second step is much harder, of course, as it requires knowledge of what style is appropriate for your field (and for the journal you are writing for), and, to some extent, it requires technical knowledge of whatever you're writing about.
The English is fine, the reviewer is just being picky
Academic articles are complex and often involve detailed theoretical or technical discussion. At times, they can be hard to follow. Sometimes this complexity is interpreted as poor language skills, and reviewers complain. I know more than one native English speaker who has received reviews asking them to check their article with a native speaker. In essence, this criticism relates to how the content is presented rather than linguistic concerns like grammaticality or phrasing.
It is not easily possible for you to determine right now which of the above scenarios has happened. However, a big help would be for you to show the manuscript to a trusted colleague who is a native speaker of English, and ask them how it reads. If the English is really atrocious, then you know you have a problem with the checking service; if there are some unusual phrases but it's otherwise fine, then you know the problem is that it's occasionally un-idiomatic; and if there are no obvious problems, then it's probably just an issue of reviewer interpretation.
The other step you should take is to re-read your manuscript and attempt to make complex exposition more clear. (This is a step I advise everyone to do at basically every stage of the writing process...) This will help your article in the case that the English was fine but the reviewer was just confused.
Finally, breathe and relax. Your article was accepted, congratulations! Clearly the reviewers and the editor thought that the scientific content was sufficient to merit publication.