I have a Lowrance 332C and LMS480M and everytime I turn on the unit it would display a message "GPS is not responding" and do not show the currently location on the GPS. The unit is hooked up to the GPS antenna. Does anyone knows what is the problem with this?

Most likely the antenna has burned out.

But I have two seperate antennas.

Have you tried switching antennas? Does it do the same for both.
Do you have a NEMA 2000 setup? if one antenna works and the other doesn't then it is the antenna. If both don't work on the unit. It's the unit. If both units don't work then go to the car parts place and buy a can of electronic clean and make sure it is not harful to plastic. then buy a can of dielectric grease. clean all connectors one at a time and then put some grease on them. If non of the above works FUBAR.

Bad terminator if there is one in the system

Like Baitman said, try switching to your other antenna on one of your units and see if it comes back up. I have 2 antennas also and had the same problem, with just one antenna on the system, it wound up being a bad tee connector. Make sure everything is still connected, fuses are good and the NMEA network is powered up. Hope this helps.