Abstract: In view of the current low-precision accuracy of ground-based GNSS tomographic water vapor, this paper proposes a method for non-uniform stratification of the vertical direction of the mesh, which improves the accuracy of the regional tomographic results. Based on multisystem GNSS observation data, the water vapor distribution over the area of 111.5～115.5° east longitude and 33.6～35.6° north latitude in Henan Province is detected by tomography, and the influence of vertical stratification method on the chromatographic results is studied. The vertical stratification method adopts uniform and non-uniform stratification methods, and the results of water vapor density are very close to those of sounding inversion. By contrast, the non-uniform tomographic data analysis shows good data accuracy in correlation coefficient, root mean square error and mean deviation. The non-uniform stratification method can obtain better atmospheric water vapor inversion results.