High temperature at reproductive stage destabilizes grain yield and quality especially in warm climate wheat production region. Breeding for heat-tolerant wheat varieties is an important target of wheat breeding in China， while identification of the molecular markers associated with the heat tolerant traits can accelerate this process. The heat-tolerant indexes of five kernel traits including thousand kernel weight， kernel length and kernel width， kernel surface area and kernel circumference were investigated by taking use of 169 wheat varieties（ lines）， and genotyping with SSR marker Xwmc44 identified three allelic variants I， II and III. A significant positive correlation between variant I and heat-tolerant indexes of four kernel traits（ thousand kernel weight， kernel width， kernel surface area and kernel circumference） was observed. The average values of heat-tolerant indexes of kernel traits in wheat varieties（ lines） with I allelic variation was greater than 1. The wheat varieties with variant II was negatively correlated with the heat tolerance index of thousand kernel weight （ P<0.01）， and negatively correlated with the heat-tolerance index of two kernel traits including kernel width and kernel circumference（ P<0.05） . The average value of heat-tolerance indexes of kernel traits in wheat varieties （ lines） with II allelic variation was less than 1. No detectable association was observed in variant III with the heat-tolerance indexes. These results showed that Xwmc44 was related to heat tolerance of wheat， and II allelic variation was a superior allele for heat tolerance of wheat. This will provide more information for heat-tolerant wheat breeding with molecular markers.