Impatiens uliginosa is a native and potential water body-restoring ornamental plant. In this study, RNA-Seq technology was used to analyze the transcriptome of its floral organs. Candidate genes related to flower color changes under copper stress were investigated through transcriptome screening, and the intrinsic mechanism of the effects of different concentrations of copper on I. uliginosa was revealed at the molecular level. The main findings were as follows: (1) Transcriptome sequencing analysis was performed on the flower organs of I. uliginosa treated with different concentrations of copper (0 mg·L⁻¹, 10 mg·L⁻¹, and 20 mg·L⁻¹). A total of 70,319 transcripts and 39,949 unigenes were obtained. An analysis of differentially expressed genes revealed structural genes including GT, ANS, CHI, and PAL; transcription factors including MYB and WD40; and transport factors including GST and ABC. (2) The gene expression levels of flower color changed in the flowering period of I. uliginosa at different copper concentrations. The expression levels of IuGT and IuGST genes in I. uliginosa were significantly different under different concentrations of copper treatments. Their expression levels were the highest at a copper concentration of 0 mg·L⁻¹ and the lowest at 20 mg·L⁻¹. In summary, the low expression of IuGT and IuGST genes was more conducive to the formation of white flowers of I. uliginosa.