Knowledge about the key traits related to genetic gains in grain yield (GY) is necessary for understanding the main yield‐limiting factors and guiding future wheat (Triticum aestivum L.) breeding. The objective of this research was to investigate the genetic progress in GY and the associated physiological traits in popular wheat cultivars released from 1969 to 2012 in southwestern China. Field experiments included eight representative cultivars that were evaluated at three experimental sites for three growing seasons. Grain yield increased at a linear rate of 0.69% or 52.52 kg ha−1 yr−1, which was mainly attributed to the increases in dry matter (DM) accumulation at maturity, harvest index (HI), and thousand‐kernel weight (TKW). The soil and plant analyzer development (SPAD) values of flag and penultimate leaves at anthesis increased with the year of release and were significantly related to GY. Significant genetic gains were made in both nonstructural carbohydrate (NSC) translocation and NSC translocation efficiency from anthesis to maturity, and there was a trend over time towards a high net photosynthetic rate (Pn) of flag leaf and canopy apparent photosynthesis (CAP) at anthesis and at 30 d post‐anthesis (DPA). In addition, the linear increases in N uptake efficiency and N utilization efficiency were both significant and positive related to GY. Therefore, these key physiological traits can be used as selection criteria for further improving yield potential. Our results also reveal the potential for using synthetic hexaploid wheat in high‐yielding wheat breeding.