The leakage calculation method and leakage mechanism of micro-pores mechanical seal are not clear. Based on the mass-conservative JFO cavitation boundary condition, a numerical calculation model was developed for the mechanical seal with micro-pores. The numerical calculation results showed that the flow rate was not equal at different cross sections along the leakage direction. Therefore, it is necessary to select a reasonable integral cross section to make the leakage calculation correct. Furthermore, the reason why the flow rate along the leakage direction is not equal was discussed through the analysis of the radial flow field, the circumferential flow field and the pressure field. It was also proposed that the leakage was reduced because the high pressure region, which was induced by the dynamic pressure and cavitation, changed the flow from leakage direction to circumferential direction. Finally, the formula and method for the leakage calculation of mechanical seal with micro-pores were presented.