Drought is an environmental factor affecting the yield and quality of rose flowers, but the potential molecular regulatory mechanism remains unclear. Here, the physiological indexes and related compound contents of rose flowers were determined under drought stress, of which flower size, fresh/dry weight, and carbohydrate accumulation were significantly reduced, whereas the contents of total phenols, total flavonoids, total anthocyanins, and volatile compounds increased compared with normal growth conditions. Transcriptome profiling identified that trehalose signaling may be involved in this process, and that the expression level of various trehalose anabolic pathway genes such as trehalose-6-phosphate synthases and trehalose phosphatases were repressed, whereas the contents of trehalose (Tre) and its precursor trehalose-6-phosphate (T6P) decreased under drought stress. Furthermore, exogenous spraying of Tre and T6P could alleviate the wilting phenomenon caused by drought stress and promote the accumulation of starch, soluble sugar, and lignin in the petals. Results indicated that T6P or Tre, as a positive regulatory signal, improves the drought tolerance of rose plants and maintains the quality of rose flowers under drought conditions, which provides new insights into the effects of drought stress on flower quality.