The chlorophyll content determines the rate of photosynthesis. To explore the genetic mechanism of the chlorophyll content, this study measured the chlorophyll content of 119 winter wheat varieties (lines) at flowering period and filling stage under watering-drought treatment. The genome-wide association scanning using 50K chips was conducted using the Q+K association hybrid model. The chlorophyll content of wheat under drought treatment was slightly lower than that under water treatment at flowering and grain filling stage. One-hundred nineteen wheat varieties (lines) were divided into three subgroups, each of which accounted for 48.7%, 23.5% and 27.7%. The polymorphic information content (PIC, Polymorphic Information Content) of the 50K chip was 0.091-0.375, and the whole-genome LD decay distance was 4.27Mb. Genome-wide association scanning (P < 0.001) identified a total of 88 loci significantly associated with chlorophyll content under the two treatments. These loci were found on all chromosomes except 4B, 5A and 7A, with a contribution rate of 9.39%- 15.69%. A total of forty-one loci significantly associated with chlorophyll content were detected at the flowering stage, among which 40 loci were identified under water treatment and one locus under drought treatment. A total of 51 loci significantly associated with chlorophyll content were detected at the grain-filling stage, among which forty-three loci were identified under water treatment and nine loci were identified under dry treatment, with a total of four repeat loci in the two stages. A locus located on 4A was detected in the flowering stage at two environments, with the contribution rate of 12.01%-12.26%. A total of 21 candidate genes associating to chlorophyll formation were identified under water treatment condition, including magnesium transporter, transporter, chlorophyllase, phospholipid/glyceryl acyltransferase family protein, GATA transcription factor. Under drought treatment condition, three genes possibly related to stable expression of chlorophyll were obtained, including chlorophyll a-b binding protein, F-box protein and dehydration stress protein, which are involved in chlorophyll synthesis and decomposition and regulate the growth and development of crops. Collectively, this study provided insights for gene cloning and marker development.