Physiological regulation is an essential way against drought stress in wheat; dissecting the genetic basis of drought-tolerant related physiological traits, and developing molecular markers can provide strong support for efficient improvement of drought tolerance in wheat. In this study, 150 doubled haploid (DH) lines derived from a cross of Hanxuan 10 × Lumai 14 were genotyped by Wheat 660K SNP Array and SSR (simple sequence repeat) markers for constructing a high density genetic map. The genetic basis of canopy temperature (CT), chlorophyll content (SPAD value) and normalized difference vegetation index (NDVI) under different water regimes at booting and mid-grain fill stages were dissected. A genetic map covering 21 chromosomes was constructed, which included 30 linkage groups and spanned 4082.44 cM, with an average interval distance of 2.20 cM. Eighty-six QTL were identified on all chromosomes except for 3D. The numbers of QTL for CT, SPAD value and NDVI are 30, 40 and 34, respectively. Seventeen QTL showed pleiotropic effects, among which, four were related to CT and NDVI, eight for CT and SPAD value, seven for SPAD value and NDVI. QPT52 located on chromosome 4D was related to all three physiological traits. The present study provided reference information and technical supports for drought-tolerant gene discovery and molecular breeding in wheat.