The chlorophyll content is one of the most important traits selected by breeders, and it is controlled by quantitative trait loci (QTLs) derived from natural variations in rice. We analyzed the QTL controlling chlorophyll content by using 94 RILs derived from a cross between 2 japonica rice cultivars, Lijiangxintuanheigu (LTH) and Shennong265 (SN265). Twenty-two QTLs controlling chlorophyll content at tillering stage, heading stage, and maturity stage were detected, respectively. Among them, Rice cv. LTH had a positive allele only at 1 locus (qCTH4) on chromosome 4. Further analysis indicated that the genetic effect of qCTH4 was the net effects within the period from tillering to heading. The QTL qCTH4 controlling chlorophyll content from tillering to heading locates between RM255 and RM349 on chromosome 4 with a LOD score 19.41, and the QTL qCTH4 explains 61.42% of phenotypic variation. In order to eliminate the influence of other QTLs, 1 single residual heterozygous plant, RH-qCTH4, was selected based on the genotypes of 114 Simple Sequence Repeat (SSR) markers. Using the segregating population derived from RH-qCTH4 by self-crossing, this region was narrowed down to an interval between RM3276 and RM17494 in an approximately 771kb target region. These results are useful for map-based cloning of qCTH4 and for marker-assisted selection of high photosynthetic efficiency variety.