Abstract: Microchannel heat sinks have become a key technology for thermal management in high-power-density electronic devices due to their efficient heat dissipation capability. However, the evaluation of cooling performance faces challenges because of the contradiction between thermal and hydraulic performance. This study takes manifold microchannel heat sinks as the research object and systematically analyzes the shortcomings of existing performance evaluation methods in balancing thermal and flow performance: single-parameter indicators cannot comprehensively reflect the coupled thermo–hydraulic effects, while multi-parameter indicators are affected by flow-rate sensitivity and nonlinear interactions, resulting in the lack of a unified basis for cross-study comparison. In view of the inadequacy of these methods in typical scenarios such as large-area temperature uniformity, high heat-flux hotspot cooling, and flow-sensitive systems, a two-dimensional evaluation framework is proposed, which is constructed from the effective heat flux under isothermal rise conditions and a comprehensive performance factor. This framework achieves unified quantification of thermo–hydraulic performance through temperature-rise standardization and heat-area normalization, avoids exponential simplifications and subjective weighting, and significantly reduces the bias caused by flow-rate sensitivity and nonlinearity. The proposed method not only improves the applicability and universality of performance comparison for microchannel heat sinks, but also provides theoretical support for structural optimization and the establishment of standardized evaluation systems.