I am working on two projects now and both of them have similar methods. What if I write the same text in the method part? Will it be count as plagiarism? I am almost finished working on them and both of them will be submitted in a different journal(one already accepted; under review, another one will be submitted soon)
I have repeated the experimental method text a lot.
Sometimes you can just cite another paper (samples prepared as described in X) but that can be inconvenient for various reasons. The method may not be very long so it is inconvenient to send reader to another paper. Or sometimes both papers are simultaneous submissions. I don't mind a citation to an "in press" or "in review" paper when you really need to--but in this case, you could and maybe should just share the details. Another case is when only small details are different. And, yes, sometimes you can say "as described in X with variations Y" but this can also become a real dog's breakfast and mystery hunt, requiring a lot of back and forth to the X paper while reading current paper.
If you want to really CYA, you could do something like, "the chemical synthesis is similar to that used in other study(ies) [citation]. And then go ahead and give the whole method.
But really, I don't think anyone will question same author recycling method text or even some intro background text. For the people who follow the area well, they are going to concentrate more on the results, regardless, and be able to skim past stuff they have seen before. For others who haven't read the whole set of papers, it can be convenient to have the methods there instead of some dog's breakfast of back forth citations.
Really...I would emphasize what you think serves the reader best. If a cite to another paper works better use that. If having the info there works better use that. I think you generally can have a hunch on this.
Reusing the text from a previous paper in a new paper is a form of "self-plagiarism" that publishers are increasingly unwilling to accept. It's true that this was a relatively common practice in the past, but the advent of plagiarism detection software has made this practice visible and publishers are starting to crack down on it.
One reason for this is that publishers want to publish "original" content and not repeat previously published material. Another reason for this is that publishers want to avoid violating copyrights owned by other publishers- the publisher of the first paper could easily sue the publisher of the second paper for copyright violation.
The way things now, chances are that when you submit the later paper you'll have it sent back to you with instructions to remove the self-plagiarism before the journal will review the paper.
Whenever "Self-Plagiarism" is a concern, you need to ask yourself
What is the main contribution to the community of this paper?
Recycling background and methodology text are probably ok. Hopefully, your methodology isn't changing that much from experiment to experiment. Academics spend years repeating the same experiments, usually only changing a few things.
From your question, it sounds like you will have a different data set per paper, which is almost certain to mean each paper can stand on its own contributions.