I am from India and I am on F-1 VISA. I am already working on CPT for one employee. Now during this employment, I did some work for one company and that company now wants me to give some compensation on 1099 form. Should I accept that form and If yes, than will there be any impact on my VISA ? Also update me with how should I file tax with 1099 form ?

You working for ANOTHER company while on CPT may have been a violation of your visa, if the work was not sanctioned by the university which you attended.

That said, you need to report the income earned regardless of whether it was a violation or not. You will file Form 1040NR with a Schedule C to report the Form 1099 income.

Thanks for your comment. I would like to inform you that I have not accepted any payment till now from the employer who wants to pay me on 1099. My CPT is completing in August. Is it OK if I accept that income after my OPT starts ? Moreover, Do I need to provide my working hours or duration while filling tax ?

You do NOT need to provide woirking hours; you just need to report the income.

If the work is with the company with whom you are doing the OPT, that will mask your violation. Note that the IRS will NOT report your outside work to the USCIS (privacy laws specifically prohibit that). Further, it is a minor violation, so if the USCUIS does find out about it, it is likely no action will be taken against you other than a letter telling you NOT to do it again.

Accept the payment and report it on your tax return as required by law.

My current and OPT employer is different and the company which wants me to pay on 1099 MISC is also different. Which I guess does not mask my violation. And If accept this income and file TAX, does it have any relation while filling H1B? Do you think it affect my H1B procedure ?

I am NOT an immigration attoryney, but, to my knowledge, this issue will not have any bearing on your H-1B visa application.

Suggest you confer with an immigration attorney to be sure.