Thermal throttling is a safety mechanism built into a machine to stop it from overheating. When the temperature of your Mac gets too high, Apple has configured it to slow down processing and performance, which will slow the rise in temperature.
If it gets even higher, the fans will kick on to cool the machine back down. Apple has decided that consumers would prefer a slow machine over a loud one, so they set the threshold to trigger the fans above the threshold for reducing performance.
You can download the free app SMC Fan Control to watch your machine's temperature and force it to run the fans.