Aiming at the uniformity phenomenon of torque output for each cylinder, the multi-cylinder non-uniformity signal quantification processing method and the cylinder uniformity control algorithm were designed based on the fuel injection control mechanism of diesel engine. Then the uniformity control model of each cylinder was developed by using Matlab/Simulink software and the validation was conducted through the model in-loop test and bench test. The results show that the control strategy can calculate the correction fuel quantities of each cylinder in real time according to the engine operating conditions and distribute the corrected fuel injection amount to each injection according to the proportion of expected fuel injection amount for each injection at the speed range between 800 r/min and 1 300 r/min with the fuel injection quantity between 2 mg/hub and 50 mg/hub. The non-uniformity of torque output for each cylinder decreases and the control strategy of uniformity for each cylinder is hence reasonable and effective.