Abstract: A set of 105 near-isogenic lines (NILs) BC4F8,BC4F9 population were developed from a backcross between Lijiangxintuanheigu(LTH,cold-tolerant landrace) and Towada (cold-sensitive cultivar,as the recipient).The genetic linkage map contains 180 simple sequence repeat (SSR) markers spanning 1820.6cM on total 12 chromosomes,with an average interval of 15.67cM.The chlorophyll contents of the rice flag leaf at booting stage were measured from three different locations (Baiyi,Xundian and Yuxi) in two consecutive years (2014 and 2015),and quantitative trait loci (QTL) were identified using inclusive composite interval mapping (ICIM) method.A total of 7 significant QTLs for the chlorophyll were identified and distributed on chromosome 1,4,5,7 and 12.The single detected QTL accounted for 11.66%—35.38% of the phenotypic variation.Among two main-effect QTLs (qCHa-1 and qCHb-7) controlling chlorophyll a and chlorophyll b contents were detected under two circumstances.These QTLs explained 21.11%—35.38% phenotypic variations with significant additive effect.The alleles for increasing traits values were from LTH,which were important functional locus to improve chlorophyll content.