The invention relates to a multifunctional ultrafast laser micromachining system and method. A frequency doubling module is arranged at the output end of an ultrafast laser, three wave band light outlets are formed in the output end of the frequency doubling module, a first light path transmission module is arranged on a first wave band output light path, a second light path transmission module isarranged on the second wave band output light path, optical beams output by the modules are combined into one beam through a beam combination lens, a first light path switching device, a second lightpath switching device and a third light path switching device are sequentially arranged at the output end of the beam combination lens, the third light path transmission module is arranged on a thirdwave band output light path, the light beam output by a third light path transmission module is located on the other light path, a fourth light path switching device, a fifth switching device and a sixth reflecting mirror are sequentially arranged at the output end of the third light path transmission module, their centers are aligned to the center of the first light path switching device, the center of the second light path switching device and the center of the third light path switching device in the vertical direction, their vertical emerging end light paths are provided with diaphragms,and processing modules are arranged at the output ends of the diaphragms. A plurality of combined processing modes are achieved.