The correlation between chlorophyll content of flag leaf after anthesis from 7 days to 24 days and 1000-kernal weight (TKW) was analysed using a RILs population from the cross between Jing411 and Hongmangchun21. In addition, the QTLs controlling these traits were also located according to the data of 2011 and 2012 crop seasons. The results indicated that the chlorophyll contents of flag leaf of 7 days (I), 14 days (II), 19 days (III) after anthesis and the total contents were positively related with TKW at the levels of 0.05 and 0.01 respectively in the two crop season. And the analysis of molecular markers linkage indicated a new QTL was found on the 2AS linked to the markers of Barc5 and Gwm448, which could explain 16.38%-20.12% (I) and 17.27%-19.35% (II) phenotype variations of chlorophyll content of flag leaf at 2011 and 2012 crop seasons respectively. Another QTL located between Barc1138 and Barc212 was only detected at 2011 crop season, which could explain 11.43% (I) and 9.67% (II) phenotype variations of chlorophyll content of flag leaf respectively. Simultaneously, the new QTL between Barc5 and Gwm448 was also confirmed to correlate with TKW and explained the variations of 13.35% (2011) and 10.14% (2012) respectively. No loci were found for the chlorophyll content of the flag leaf at other stags after anthesis.