The cotton direct seeding after wheat (rape) harvested is under trial and would be the future direction at the Yangtze River Valley region of China. The objective of this study was to quantify the effects of branch and stem architecture on cotton yield and identify the optimal cotton architecture to compensate the yield loss due to the reduction of individual production capacity under high planting density in the direst seeding after wheat harvested cropping system. The characteristics of the stem and branch architecture and the relationships between architecture of the stem and branch with yield formation were studied on eight short season cotton cultivars during 2015 and 2016 cotton growth seasons. Based on the two years results, three cultivars with different architectures of stem and branch were selected to investigate the effect of mepiquat chloride (MC) application on the architecture of the stem and branch, boll retention, and the yield in 2017. Significant differences were observed on plant height, all fruiting nodes to branches ratio (NBR) in the cotton plant, and the curvature of the fruiting branch (CFB) among the studied cultivars. There were three types of stem and fruiting branch structures: Zhong425 with stable and suitable plant height and NBR (about 90 cm and 2.5, respectively), high CFB (more than 10.0), and high boll retention speed and seed cotton yield; Siyang 822 with excessive plant height and NBR, low CFB, and low boll retention speed and seed cotton yield; and other studied cultivars with unstable structure of stem and branch, boll retention speed, and seed cotton yield across years. And MC application could promote the appropriate plant height and NBR and high CFB and thus resulted in high boll retention speed and the yield. The results suggested that the suitable plant height and NBR (about 90 cm and 2.5 respectively), and high CFB (more than 10.0), which was related to both genotype and cultural practice, could promote the higher boll retention speed and seed cotton yield.