To solve the low efficiency of oxygen mass transport and weak performance of self-breathing micro-direct methanol fuel cells (μDMFCs), the different cathode current collectors with a perforated structure were designed. Firstly, the effects of opening shapes and opening ratios on the cell performance were studied by establishing the cathode model of μDMFC,which indicates that the opening shapes have little effect on the cathode current density, and the variations of cathode current are rather small in the range of opening ratios. Then, experiments were performed to verify the simulations. Based on the above analysis, a cathode perforated structure with parallel channels was presented. Compared with conventional structures, the simulation results illustrate that the improved structure can effectively improve the oxygen mass transport to increase the cell performance. A self-breathing μDMFC with the active area of 8 mm×8 mm was fabricated on the stainless steel plates by utilizing micromachining technology. Test results show that the peak power density of the μDMFC is 11 mW/cm2 with methanol solution of 1 mol/L and speed of 1 ml/min at room temperature. In conclusion, the improved self-breathing cathode structure can be contribute to further development of portable micro power source systems.