Subsurface chlorophyll maxima (SCM) are found in stratified lakes, reservoirs, and oceans. Spatial variations of the SCM magnitude, depth, and thickness during stratification and related factors were examined in a large, deep subtropical reservoir, Lake Qiandaohu. Significant spatial differences in the SCM parameters were found throughout the lake as thermal stratification developed in the late spring of 2014. SCM depth and thickness were positively correlated with euphotic depth and mixed layer depth but negatively correlated with epilimnetic nutrient concentrations. SCM magnitude was negatively correlated with euphotic depth and mixed layer depth and positively correlated with epilimnetic nutrient concentrations. Seasonal variations in SCM differed among subregions of the lake, which were related to seasonal differences in environmental parameters. SCM (averaging 66.2 mg/m2 in spring and 96.4 mg/m2 in summer) accounted for about 82% of the total areal chlorophyll of the water column (Tchl), and the SCM magnitude was better correlated with Tchl than the surface chlorophyll concentration. This study contributes to understanding of factors causing spatial variations in of SCM in the deep subtropical lakes.