For the technical problem of microgroove bottom finishing in microchannel hydrogen production reactor, ultrasonic vibration assisted magnetic composite fluid (UMCF) polishing technology were carried out. According to the surface contact theory, the influence of gas film at the bottom of the microgrooves on the magnetic composite fluid (MCF) polishing was analyzed, and the surface quality of the bottom of the microgrooves was improved by introducing ultrasonic vibration. The effect of UMCF polishing on the bottom of microgrooves was investigated by experiments. The effects of MCF and UMCF polishing on the surface morphology, surface roughness and removal rate of the microgrooves under different parameters were obtained. The results show that at the particle size of carbonyl iron powder of 48 μm, polishing time of 5 min, polishing wheel speed of 500 r/min, polishing gap of 2 mm and amplitude of 5 μm, the polishing effect is the best. The top surface roughness of the microgrooves reaches 0.217 μm. The bottom surface roughness reaches 0.403 μm, and the removal rate is 4.74 mg/min. Experimental results provide guidance for ultrasonic vibration-assisted magnetic composite fluid polishing of microgroove structure parts.