A case-control study is performed in this paper to explore various possible effects and clinical value of the photodynamic therapy combined with thymosin for the treatment process of the condyloma acuminatum (CA) in the anal canal. For this purpose, a hundred (100) patients specifically with CA in the anal canal who were regularly treated in the hospital from February 2019 to April 2021 were recruited. The first group, that is, the control group, was treated with thymosin, whereas photodynamic therapy combined with thymosin was used as a treatment for the study group. The curative effect, clinical index, LTN, SP, TGF-β 1, TNF-α, CD3+, CD4+, CD8+, and the adverse reactions of incidence were compared between these groups. Moreover, 27 cases were observed to be obviously effective, 22 were observed to be effective, and a single case was observed to be ineffective. Thus, 98% is the total effective rate where a single case relapses. Likewise, in the control group, 15 cases were observed to be obviously effective, 28 effective, and 13 ineffective. Thus, 86% is the total rate of effectiveness where thirteen (13) cases relapse. We have observed that the study group has a higher rate of effectiveness than the control group and the rate of recurrence of the former group was slightly lower than that of the latter group, that is, the control group (P 0.05).