With the nitrochlorobenzene binary eutectic system and naphthalene-benzathiophene solid solution system, the purification process of tower crystallizer under continuous flow was investigated. Under the optimal conditions, the p-nitrochlorobenzene and naphthalene were purified to over 99.99%. Moreover, the theory of the purification process is analyzed. Based on the fact that the rate of purification flow at the cross section of the column was equal to the rate of removal of impurities at the bottom of the column, a mathematical model of continuous multistage countercurrent fractional crystallization process was established. Comparing the calculated data with the experimental data, the results demonstrate that the theoretical model can well describe the mass concentration distribution in the tower crystallizer. Appropriate reflux ratio and stirring are necessary to achieve an ideal equilibrium state at a certain crystal bed height. It provides basis for the industrial application of tower crystallizer.