The research on the spatial structure and mathematical statistic of the crossregional population flow is obviously insufficient, especially the statistical research on the operation law of the population migration data itself and the internalization process of the data is very rare. In this article, description, model expression and prediction are three separate systematic processes which should not be separated in the study of spatial flow structure of population migration. In view of this, this paper integrates the “ basic formula ” of descripting, modelling and predicting the spatial structure of migration flows: multiplicative component model, log-linear model and bi-proportional adjustment method are used to describe, model and predict the spatial structure characteristics of migration flow in China. From the perspective of demographics, the empirical process applies the data of China Migration Dynamics Survey from 2011 to 2017 and the three census data from 2000 to 2020, and takes the population migration between the 11 provincial areas in the Yangtze River Economic Belt and the four major regions of China’s east, central, west and northeast flows as an example. Based on the endogenous law of the migration flow matrix and the data self-generation process the spatial structure of cross-regional population migration flow in China is studied comprehensively. The main results show that the contingency table and its endogenous multiplicative component model can well describe the population migration flow with a two-dimensional structure. The unsaturated log-linear model with four-parameter [O D A OA] can describe the cross-regional main characteristics of the population flow structure in China, with a fitting degree reaches 82%. The prediction of migration flow is of great significance, but the exploration is insufficient. The two sided proportional adjustment method can be used as a good tool for the population migration flow prediction. The main purpose of the article is to introduce and build a system framework or basic program for the study of the spatial structure of population migration, and to promote the research and application of spatial statistics or spatial population in China.