I came from China at Sept,2007, with F2 visa. I became a postdoctor in university this year, and changed to H1b in Jan, 2009. Because of US-China treaty, I don't need to pay Fed and state tax. But, I paid medicare and social security tax. I heard the postdoctor with J1 visa don't need to pay medicare and security tax. I am wondering if I can also waive it in my first employment year?

On H1-B you must pay SS tax, Medicare tax and income taxes. Read about H1-B: Your U.S. Tax Return: The U.S. Visas

Under U.S. law, FICA (Social Security and Medicare) taxes become payable after two calendar years inside the U.S.