Application requirements for avionics are often very strict. For example, the heat sinks of avionics need very good temperature uniformity, but the flow rate of coolant is very restricted. In addition, the use of micro-channels is not recommended due to the potential clogging issue. Considering these design requirements, we will discuss a multiple-objective optimal design method to obtain a good stacked mini-channel structure for avionics applications. In our thermal design, the design variables are the mini-channel geometry parameters. Temperature uniformity, entropy generation, max temperature of heat sink and pump work are chosen as the objective functions. A Multi Objective Genetic Algorithm (MOGA) and Fluent solver are used together to minimize multiple objective functions subject to constraints, and locate the Pareto front. By analyzing the multiple objective optimal results, we can draw the conclusion that the objective functions of T max and s g have same effect on the optimization, and the multiple optimal results are a set and not a single value. If mostly focusing on the temperature uniformity, we can recommend some optimal structures to design a stacked mini-channel heat sink.