Leaf area index (LAI) during the growth process is one of the most important indexes for monitoring high-yield cotton production, but the present use of LAI is limited due to the varying photosynthetic capacity of cotton leaves at different plant positions and growth periods. Thus, a more accurate leaf area-related index that includes both leaf area and photosynthetic capacity was explored herein based on the contribution to final yield and photosynthetic efficiency in directly seeded short-season cotton following wheat cropping in the Yangtze River region of China. Pinhead-squares were labeled to investigate the critical timing of pinhead-square appearance during yield formation from 2015 to 2019, and the photosynthetic characteristics of the corresponding subtending leaves were measured in 2017 and 2018. The results showed that the pinhead-squares that appeared after 64 days before frost (DBF) did not contribute to yield (the bolls failed to open at harvest). Furthermore, the sucrose phosphate synthase (SPS) and soluble acid invertase (SAI) activities, carbon assimilation rate (Pn), and 14C photosynthate exportation of the corresponding subtending leaves also declined markedly after 20 DBF. Therefore, the subtending leaves of the pinhead-squares that were formed before 64 DBF were defined as effective leaves based on their contribution to final yield, and their leaf areas were correspondingly defined as effective leaf areas. To further explore the contribution to yield, high-efficiency and low-efficiency leaves would exist among the effective leaves according to the load capacity of the reproductive organs (the presence or absence of corresponding subtending reproductive organs. Among the effective leaves, the subtending leaves with loaded bolls exhibited higher Pn, SPS and SAI activities, and 14C assimilate exportation and were defined as high-efficiency leaves, and their leaf areas were defined as high-efficiency leaf areas. Different effective LAI and high-efficiency LAI cotton populations were constructed using five sowing dates and five nitrogen application rates to assess the relationship between effective LAI, high-efficiency LAI, and seed cotton yield in both 2018 and 2019. With increased effective LAI and high-efficiency LAI, higher seed cotton yields were detected. These results suggested that enhancing effective and high-efficiency leaf area, especially for high-efficiency leaf area, benefits seed cotton yield in cotton production.