Taking intermittent high-pressure transesterification reactor as object, the influence of background pressure and temperature on thermal equilibrium state of the water were discussed. Through establishing 3-D temperature-pressure field analysis model, the high-pressure hydrothermal state control equation was determined and supercritical state reaction condition was optimized. On this basis, the experimental study on biodiesel prepared with large-scale aquaculture microalgae as raw materials was carried out and the oil quality was analyzed. The results indicated that the output rate of biodiesel prepared with chlorella was evidently higher than that of other types of algae. The introduction of supercritical state reaction condition almost doubled the output rate of biodiesel and the oil quality had nearly the same carbon/hydrogen mass ratio, calorific value and density with the 0# diesel.