my pc has two disks. one has fedora9 linux and another one has windows. How to sync the time between the two?.
Are you running vmware?
time is set and maintained by the kernel in both cases - time.windows.com is the timeserver for windows, use that to get a correct time setting right after you boot windows.
Use one of NTP timeservers NIST Internet Time Service for Fedora. setup xntpd (see the man page) if you leave the system up for really long periods of time.
try syncing them with ntp.