The combination of subsurface pipe drainage and paddy field flooding is a widely used method of soil amelioration for saline and alkaline land. In order to explore the salt drainage effect of combined application of subsurface pipe drainage and flooding in paddy fields, we monitored the variation of soil salt content in the paddy field with subsurface pipe drainage of 120 hm2 in Hetao Irrigated Area in Inner Mongolia before and after three drainages. Based on the geostatistics, the spatial variability of regional salt before and after drainage was analyzed, and the law of salt drainage in different growth periods was summarized. The results showed that the subsurface pipe drainage promoted the homogenization of soil salt in the paddy field. After three times of drainage, the coefficient of variation were 35.66%, 30.85% and 29.43% respectively, showing moderate variation; and the spatial structure ratio decreased by 54.3%, 77.7% and 5.2% respectively, which indicated that the continuous strengthening of internal factors resulted in spatial autocorrelation of the soil. Due to the influence of water demand characteristics in different growth periods, the fractal dimension relationship of three drainages was D2>D1>D3. After the drainages, the soil salt content was transferred from high salt heterogeneity to low salt homogeneity. Before the drainages, the salt content of soil was less than 7.8, 8.0, and 6.2 g/kg respectively, which decreased to 2.0-5.8, 2.4-6.6, and 1.1-4.8 g/kg after the drainages. Most of the sample points in the area developed towards the direction of homogenization. The salt content of the first drainage (on April 16) was less than 9 g/kg, and the desalination rate was positively correlated with the initial value. The desalination rate of the second (on July 16) and the third (on September 6) drainage increased with the increase of salt content. According to the quantitative analysis of the transformation process of high salt to low salt, the area of heavy saline soil decreased by 69.12%, the area of light and medium salted soil increased by 20.99% and 51.15%, and the distribution of different grades of soil in different depths were similar, showing the trend of high in northeast and low in southwest. The closer to the strong drainage pump station, the higher salt content of the soil. The research results can provide some reference for the improvement of saline and alkaline land and efficient use of land resources in Hetao Irrigated Area of Inner Mongolia.