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A modified 3D numerical model on the energy conversion process in the anode side of a Direct Methanol Fuel Cell (DMFC) system was constructed and validated to published experimental results. Systematic simulations were performed to investigate the underlying mechanisms of the energy conversion process, and the combined effects of inlet flow rate and input methanol concentration were summarized systematically. The increase of flow rate was found to be an effective strategy to accelerate the internal flow fields, while the diffusion layer was proposed to be a critical component in the design of high-performance DMFC. The frontier for optimal conditions of DMFC’s output was also determined, which can be helpful to improve the energy conversion performance of DMFC in practical applications.