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A numerical simulation model of embedded liquid microchannels for cooling 3D multi-core chips is established. For the thermal management problem when the operating power of a chip changes dynamically, an intelligent method combining BP neural network and genetic algorithm is used for distribution optimization of coolant flow under the condition with a fixed total mass flow rate. Firstly, a sample point dataset containing temperature field information is obtained by numerical calculation of convective heat transfer, and the constructed BP neural network is trained using these data. The “working condition–flow distribution–temperature” mapping relationship is predicted by the BP neural network. The genetic algorithm is further used to optimize the optimal flow distribution strategy to adapt to the dynamic change of power. Compared with the commonly used uniform flow distribution method, the intelligently optimized nonuniform flow distribution method can further reduce the temperature of the chip and improve the temperature uniformity of the chip.