Objective To compare the clinical efficacy and safety of bovine basic fibroblast growth factor gel (bFGF) and modified chitosan wound-healing emulsion in treating skin ulcers. Methods Selecting 80 patients with skin ulcers in our hospital from May 2022 to May 2025 as the research subjects, they were randomly divided into an observation group and a control group using a random number table method, with 40 cases in each group. The control group was treated with bFGF, while the observation group was treated with modified chitosan wound repair gel. The efficacy, wound healing rate and time, inflammatory factor levels, scar score (VSS), and quality of life score (QOL) before and after treatment were compared between the two groups, along with adverse reactions during follow-up. Results The total effective rate of the observation group was 95.00%, which was higher than the 80.00% of the control group, and the difference was statistically significant (P<0.05); The wound healing rate of the observation group was shorter than that of the control group, and the wound healing rate was higher than that of the control group (P<0.05); After treatment, the levels of inflammatory factors in both groups decreased, with the observation group being lower than the control group (P<0.05); Both groups showed improvement in VSS and QOL scores after treatment, with the observation group outperforming the control group and the difference being statistically significant (P<0.05); The incidence of adverse reactions in the observation group was 5.00%, which was lower than the 20.00% in the control group, and the difference was statistically significant (P<0.05). Conclusion Compared to bFGF, modified chitosan wound-healing emulsion effectively inhibits local inflammation, optimizes the wound healing microenvironment, accelerates skin ulcer wound healing, and offers higher medication safety.