The flower and pod abscission is one of the characteristics of soybean that severely limits yield, especially when intercropped with maize. Therefore, suitable soybean cultivars for intercropping are urgently needed to improve farmland productivity. We conducted a two-year field experiment to evaluate the flower and pod abscission, dry matter production, and yield advantages of 15 soybean cultivars. The results of the principal component analysis (PCA) and cluster analysis (CA) showed that 15 soybean cultivars were classified into three groups, i.e., high-yielding group (HYG), mid-yielding cultivars (MYG), and low-yielding cultivars (LYG). In the HYG group, ND12 and GX3 had characteristics of more flowers and pods and less abscission of flowers and pods. Moreover, the net assimilation rate (NAR) and relative growth rate (RGR) of HYG were significantly higher than the other. The HYG obtained a considerably higher partition ratio of 53% from biomass to seed than the other. Therefore, selecting and breeding cultivars with the characteristics of more flowers and pods and less abscission of flowers and pods can help to increase soybean yield in intercropping.