With the popularization and development of drip irrigation under film, the problem of secondary soil salinization in Xinjiang is becoming more and more serious. To explore water and salt transport in drip irrigation under mulch and drainpipe drainage, drainage tests of drainage ditches in saline-alkali soil in the Xinjiang 112 group were used to monitor soil salinity changes by controlling field irrigation. Then, a HYDRUS (PC-Progress, Prague, Czech Republic) numerical model was used to simulate and analyze the changes in salinity during cotton growth and the autumn salt return stage in saline-alkali soil under drainage conditions. The agreement between the simulated and measured values was high, and the model parameters were reliable. During the growth period of cotton, the salinity continued to decrease, and the salt began to return after the harvest. Compared with before planting, in the 0–80 cm soil layer, the average desalinization rate reached 43.52% under the mulching films, and the average desalinization rate reached 13.83% under and between the mulching films. After the cotton was harvested, salt returned to the upper layer of soil. However, it still showed a decrease compared with the level before sowing. The average salt content of 0–80 cm soil decreased by 5.14%, and the average salt content of 0–200 cm decreased by 2.60%. This shows that the total salt content in soil will continue to decrease after long-term use of drip irrigation and underground pipe drainage.