Abstract: Based on the charge repulsion and solution-diffusion effect in nanofiltration separation, the correlation among mass transfer behavior, solution environment and molecular structure of three typical alkaloids from medicine was analyzed by nanofiltration mass mathematical model. The experiment revealed a linear relationship between ln(1-R_o)·J_v/R_o and J_v, and the regression coefficients were all greater than 0.9. Compared with the ultrafiltration separation behavior conforming to molecular sieve, the mass transfer coefficient of three alkaloids under different pH was pH 3.00 < pH 7.00 < pH 10.00. As the pH changed, the state of alkaloid transit from ionic state to a free state, the alkaloid could easily approach the membrane surface and pass through the nanofiltration membrane with charge repulsion and solution-diffusion effects, and the results were verified by the membrane adsorption tendency. The nanofiltration mass transfer of alkaloids is related to the state and molecular weight. In the ionic state, the charge effect produces separation behavior, and the molecular state is related to the molecular weight. The separation mechanism of nanofiltration for alkaloids was clarified further by analyzing the correlation of nanofiltration mass transfer behavior and molecular structure. The results of nanofiltration technology provide references for separation of alkaloids at room temperature with fast separation and low energy consumption.