Objective To explore the efficacy and safety of Fuzheng Xiaoji recipe in the treatment of colorectal cancer based on the subcutaneous transplanted tumor model in mice. Methods The subcutaneous tumor transplantation mouse model was established and the mice received Fuzheng Xiaoji recipe treatment, which could strengthen the body resistance and eliminate stagnation. The high-throughput transcriptome sequencing technology was used to evaluate treatment effect. The differentially expressed genes were annotated through Ensembl, gene oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and the related biological functions of abnormally expressed genes were compared and analyzed. Hematonylin and eosin （HE) staining was used to observe the effect of Fuzheng Xiaoji recipe on liver and kidney of tumor-bearing mice. Results Tumor volume and weight in both the low-dose and high-dose groups of Fuzheng Xiaoji treatment were significantly lower than those in the control group (P<0.001). Transcriptomic analysis revealed 166 upregulated and 328 downregulated genes in the tumor tissues after Fuzheng Xiaoji recipe treatment. Hierarchical clustering analysis, based on transcripts per million (TPM) values, demonstrated significant differences in gene expression between the treatment group and control groups. KEGG pathway analysis indicated that the top 20 enriched metabolic pathways included the calcium signaling pathway, cyclic guanosine monophosphate (cGMP)-protein kinase G signaling pathway, and cyclic adenosine monophosphate (cAMP) signaling pathway (P<0.05). HE staining results showed there were no significant hepatotoxicity or nephrotoxicity in Fuzheng Xiaoji recipe treated mice. Conclusions Fuzheng Xiaoji recipe could reduce the growth of CT26 subcutaneous transplanted tumors in a dose-dependent manner in mice, and it didn’t show obvious hepatorenal toxicity. Transcriptome analysis showed that the therapeutic effect of Fuzheng Xiaoji recipe on colorectal cancer may relate to regulating the proliferation of colorectal cancer, inducing apoptosis of colorectal cancer cells and inhibiting tumor migration and invasion.