To improve the non-uniformity of a multi-cylinder marine diesel engine caused by manufacturing assembly errors and performance degradation of the fuel injection system, with the instantaneous speed applied as the control target, the feedback variable of each cylinder’s exhaust temperature was used to obtain the non-uniformity information and the injection quantity of each cylinder was applied as the control variable; the inhomogeneity control was accomplished by modifying the injection pulse spectrum. The model of AVL Cruise M was established and validated by bench test data. The non-uniformity control strategy based on the instantaneous speed and the exhaust temperature of each cylinder was developed in SIMULINK, and the control effect was compared with the closed-loop control of cylinder pressure by software in-loop simulation. The results showed that the non-uniformity control strategy based on exhaust temperature could significantly improve the uniformity of each cylinder; although the improvement effect was not as great as the non-uniformity control strategy based on cylinder pressure, the cost was significantly reduced, and the practicality and reliability were better. With the closed-loop control of exhaust temperature and instantaneous speed, the CV (Coefficient of Variation) of IMEP (indicated effective pressure) was close to the closed-loop control of cylinder pressure; the maximum occurred at 25% load when it was 0.199%. This co-simulation provided a theoretical basis for the subsequent hardware-in-the-loop simulation and actual engine tests.