Provided are a main control system and a device for a nuclear magnetic resonance logging while drilling tool, the system includes: a digital signal processor, an auxiliary measurement module, a pulse signal generation module and a memory disposed in a downhole drilling tool; wherein the digital signal processor is communicatively connected to an upper computer arranged on the ground, the auxiliary measurement module and the pulse signal generation module respectively; the memory is communicatively connected to the pulse signal generation module. The main control system and a device for a nuclear magnetic resonance logging while drilling tool achieve the effect of improving the accuracy of the logging data.