The vascular bundle plays a vital role in photoassimilates transportation in rice. However, the vascular bundle characteristics of basal internode and its relationship with stem assimilates allocation and yield remain unclear. In this study, experiments with four different types of rice varieties subjected to three nitrogen application levels were conducted. The results showed that large vascular bundles (LVB) and small vascular bundles (SVB)-related traits of basal internode exhibited genotypic differences. Indica-japonica hybrid varieties had the highest number of cross sectional areas and phloem areas of LVB and SVB, thus the highest stem nonstructural carbohydrates (NSC) translocation, grain filling percentage and grain yield, followed by indica hybrid varieties and indica conventional varieties, and those were the lowest in japonica conventional varieties. The LVB and SVB related traits were significantly and positively correlated with stem NSC translocation, grain filling percentage and grain yield, respectively These results suggested that improving the characteristics of basal internodes was beneficial to enhance stem NSC translocation and consequently increase grain yield. Nitrogen application increased LVB and SVB related traits. Therefore, varieties with developed vascular bundles of basal internodes and cultivation techniques for improving vascular bundle related traits should be considered as the effective route for increasing grain yield.