Sand wave geometry affects flow structure, sediment transport and movable bed roughness. In this study, a multi-beam sounding system was used to measure the detailed topography of a typical sub-reach in the Upper Jingjiang Reach for the first time. An existing quantization algorithm of sand wave geometry was improved to calculate and determine various geometric parameters of sand wave, and variation characteristics of sand wave geometry were analyzed under different flow intensities. The results indicated that: (i) the average heights of small and large sand waves in the study reach were 0.16-0.81 m and 0.96-2.31 m, respectively, while the corresponding wavelengths were 13-27 m and 16-41 m. The scale of sand wave was small, as compared with the magnitude of water depth, and the heights of small and large sand waves were less than 0.045 and 0.150 times of water depth respectively; (ii) the angle of leeside slope was basically less than 14° and less than the submerged repose angle of sediment. The relationship between leeside slope and steepness was well described by the linear equation; (iii) medium-to-flood flows had a stronger shaping effect on geometric scale of sand wave than low flows, and had a stronger shaping effect on large sand waves in shallow water depths than in deep water depths. This study quantified the sand wave geometry in natural rivers, and also demonstrated the geometric characteristics of sand wave. It provides a perspective for the quantification, statistics and analysis of sand wave geometric parameters in large alluvial rivers.