The invention discloses a fiber and lithium niobate wafer pneumatic pressurized grinding mechanism and grinding method, including a three dimensional positioning device, a pneumatic device, and a clamping mechanism, a z-axis moving mechanism switching board of the three dimensional positioning device is connected with the pneumatic device, and the clamping mechanism is arranged on the pneumatic device. A fiber and lithium niobate wafer is clamped by the clamping mechanism and is connected with a cylinder piston rod through an adjusting slide rod and a beam type force transducer. The three dimensional positioning device can realize the accurate positioning and grinding micro-feeding of a lithium niobate wafer clamping tool, the pneumatic device makes the change of the grinding pressure a gradually changing process, and the lithium niobate wafer clamping tool can stably and rapidly clamp a lithium niobate wafer. The grinding pressure during the grinding of the lithium niobate wafer is constant, and the changing process of the grinding pressure is a gradually changing process, so that the grinded end face quality is guaranteed, and the grinding process is stable and reliable; and meanwhile, the fiber end face of the grinded lithium niobate wafer can be conveniently observed.