Boron (B) deficiency is common in some cotton (Gossypium hirsutum L.) growing regions of the world. A better understanding of changes in the growth and physiological characteristics of cotton plants during the development of B deficiency will help us to define field diagnosis techniques and improve B fertilizer management recommendation. An experiment was conducted in a controlled-environment growth chamber to determine effects of B deficiency during early vegetative growth on leaf photosynthesis, plant dry matter accumulation, photosynthetic assimilate partitioning, and other physiological parameters. Boron deficiency considerably decreased leaf net photosynthetic rate, plant height, leaf area, fruiting sites, and dry matter accumulation during squaring and fruiting. Depressed photosynthesis and plant growth (especially fruits and roots) resulted in increased fruit abscission and changes in dry matter partitioning among plant tissues. The results help explain effects of B deficiency on suppression of cotton growth and yield and provide information for improving the diagnosis of B deficiency in cotton production.