This study aimed to explore the molecular mechanism of foot color difference to guide the selective breeding of high-quality Paphia textile. In this study, the foot transcriptomes of P. textile with different colors were analyzed by the second and third-generation sequencing technology. Analysis of gene differential expression was also performed in the orange and the white feet of P. textile. The second-generation sequencing results showed that a total of 44.82 Gb of clean data were obtained from six samples, GC content was 35.30%-38.21%, and the percentage of Q30 base was 94.43% or above. The results of third-generation sequencing showed that the orange foot group and light white group obtained 16 968 and 21 611 high quality transcripts, respectively. Among them, high quality transcript sequences were compared with the major databases, 5058 full-length transcripts with annotated information were obtained. Three generation full-length transcripts were regarded as reference sequences, and the second-generation data were aligned back to the reference sequence. A total of 57 differentially expressed transcripts were obtained, including 34 up-regulated and 23 down-regulated genes in orange group. 12 randomly selected transcripts were validated with realtime fluorescence quantitative PCR (qPCR), which showed that they were consistent with the qPCR analysis results. Subsequently, through bioinformatics analysis, it was found the regulation of foot color was affected by fatty acid biosynthesis and metabolism, muscle composition, energy metabolism energy metabolism in P. textile. Among them, peroxisome proliferators-activated receptors (PPARs) regulated fatty acid biosynthesis and metabolism. Troponin is an important component of muscle. Arginine kinase (AK) is involved in energy supply during pigment deposition. It is speculated that PPARs, Troponin, and AK play an important role in the pigment deposition. The results of this study may pave the way for further exploring the molecular mechanism of color-related genes and assist selective breeding practices in P. textile.