I am planning on working under a professor after my UG completes. However the professor has said that it would be an informal arrangement between the two of us, as the formal process is a bit complicated and would require intervention from the institute. So, the question is, could I take on this offer and get a certificate from the professor(of course signed by him) and state it as a work experience in my CV?
Your work with the professor is valid work experience and possible research experience, depending on what is involved. But a "certificate" is of less value to you than a LOR. The reason is that the letter comes direct from the professor and so has implied credibility, whereas something that you provide, even if honestly, is open to question. Even if it isn't disbelieved (and it probably won't be) it will be given less weight.
Let the professor know that you will, in the future (soon or later) be needing letters to continue your education. Some time to reflect will probably mean a better letter.
If some publication comes from your work, you may not qualify as a co-author, but try to get an acknowledgement in the paper if possible. Ask for it explicitly, I think. Even better to be a co-author, of course. But, make sure, in any case, that you have a record of the publication and that the prof is willing to say, in a LOR, that you contributed to the project.