Mass transport behaviors in passive micro direct methanol fuel cells (μDMFCs), including methanol mass transport at the anode and gas-liquid two-phase mass transport at the cathode, are essential during the actual working process. However, these mass transport behaviors also face serious problems, such as methanol crossover mass transport and gas-liquid two-phase mass transport obstruction, which significantly reduces the performance of passive μDMFCs, restricting their application greatly. Herein, we propose an improved multi-substance mass transport mechanism dominated by water mass transport. The proposed mechanism is established by constructing a hydrophilic mass transport layer (MTL). Theoretical analysis shows that mass transfer behaviors under the proposed mechanism are better than those under the conventional one, thus improving cell performance. Based on this, the proposed mechanism is applied to passive μDMFCs in real scenes by preparing hybrid nanomaterials to construct the MTL. As a result, the performance of novel μDMFCs with the proposed mechanism is greatly improved. The power density of the novel μDMFCs reaches nearly two times that of conventional ones, and the energy density reaches about 6.2 times under high-concentration methanol fuel. The comprehensive study on the mass transport mechanism of passive μDMFCs aims to provide theoretical reference and practical experience for promoting their wide application.