Objective: To optimize the drying characteristics of dragon fruit freeze-drying process. Methods: Based on the fractal theory and the theory of heat and mass transfer in porous media, the COMSOL software was used to numerically simulate red pitaya slices with a thickness of 8, 10, 12, 14 mm and a radius of 40 mm to simulate the sublimation and drying stage of pitaya. The heat and mass transfer process in the internal porous medium, the real-time displacement of the ice interface during the ice sublimation process is obtained, the sublimation period is predicted, and the experimental verification is carried out. Results: The simulated data were in good agreement with the experimental data, and the error was small. The maximum relative error of dehydration rate was 12.6%, and the absolute error was 0.18 g/h; the maximum absolute error of water content was 5.4%. Under the same initial quick-freezing temperature, with the increase of thickness, the time of sublimation drying stage increases nonlinearly; the larger the pore diameter of dragon fruit, the larger the effective diffusion coefficient, the faster the drying speed, and the lower the product quality. Conclusion: Based on the fractal theory, a good numerical simulation of the freeze-drying process of dragon fruit can be achieved, and 10 mm is the optimal thickness of red dragon fruit.