Hello, I am currently in OPT.
My employer does not withheld social security tax from my pay check.
Maybe he thought that I am nonresident alien. But it has been turned out I am RESIDENT ALIEN.
Since I have been in US since 2004, and never been back to my country.
How should I resolve this? Now I know I am subject to social security tax.
Should employer amend Form 941 and pay my social security tax?

Thanks in advance.

But it has been turned out I am RESIDENT ALIEN.
Since I have been in US since 2004, . . .The exemption does not apply to you, F-1 visa holder, a nonimmigrant, who became resident alien in 2009.
"How should I resolve this?"---You need to contact your employer so that he/she can start deducting(withholding) your FICA taxes, and he/she also collects it from full year. For past yearFICA taxes, 2009, I guess, the IRS will question your employer. Then he/she will contact you to collect the back taxes. Or you can let your employer know this.
"Should employer amend Form 941 and pay my social security tax?"----as you said, your employer should complete the 941X, amendment form for the federal 941 Form.

Thank you so much

Actually, wnhough does not quite have it right.

The IRS will NOT bother you at all about the FICA taxes for 2009. The IRS policy is such matters has been consistent for 60 years: the EMPLOYER is responsible to collect the required taxes, and then collect the employee's share as needed.

However, they CANNOT collect the previous year's taxes after the 31st of January of the following year, so you are NOT liable for 2009, nor will the IRS EVER hold you liable.

They likely WILL hold the employer liable, because they expect the employer to ask relevant questions, such as "How long have you been in the United States under your current visa?"

You may feel that you have the ethical responsibility to pay your share of the 2009 taxes. That is up to you, but you have no LEGAL requirement to pay the 2009 taxes.