Objective To investigate the clinical effect of rectal administration of Neiyi Zhitong Prescription in the treatment of endometriosis dysmenorrhea and its effect on serum levels of cancer antigen 125 (CA125) and vascular endothelial growth factor (VEGF). Methods A total of 60 patients with endometriosis dysmenorrhea were randomly divided into treatment group and control group, with 30 patients in each group. The patients in the treatment group were given enema with Neiyi Zhitong Prescription, and those in the control group were given oral Sanjie Zhentong Capsule. Each course of treatment was 15 days, and both groups were treated for 3 courses. The clinical outcome and the changes in CA125 and VEGF after treatment were evaluated after three months of follow-up. Results Both groups had significant reductions in serum levels of CA125 and VEGF after treatment (P<0.05), and the treatment group had significantly greater reductions than the control group (P<0.05). The treatment group had a significantly better clinical outcome than the control group (P<0.05). Conclusion Neiyi Zhitong Prescription has a marked clinical effect in the treatment of endometriosis dysmenorrhea by reducing serum levels of CA125 and VEGF.