Objective To compare the reparative effects of moxibustion at “Guanyuan” and “Shenshu” points in rats with a thin endometrium. Methods Thirty-two female Sprague-Dawley rats were divided randomly into control(CON), model(MOD), Guanyuan(GY), and Shenshu(SS) groups. A thin endometrium model was established using 95% anhydrous alcohol. The Guanyuan and Shenshu groups underwent moxibustion at the Guanyuan and Shenshu points, respectively, and the other two groups of rats were fixed in the same way. Temperature changes at the acupoint area were measured at different time points. The pathological morphology of the uterus was observed by hematoxylin and eosin (HE) staining, and serum levels of inflammatory factors and hormone levels were detected by enzyme-linked immunosorbent assay (ELISA). Expression levels of proliferation and endometrial receptivity factors were detected by immunohistochemistry (IHC), and angiogenesis factors were detected by Western blot. Results The temperatures immediately after moxibustion and after 5 min were higher at the Shenshu compared with the Guanyuan acupoint (P<0.01). Endometrial thickness and numbers of glands and blood vessels were decreased in the MOD group compared with the CON group (P<0.01), serum interleukin 1β (IL-1β) was increased (P<0.01) and PROG was decreased (P<0.01), and Ki67, proliferating cell nuclear antigen (PCNA), leukemia inhibitory factor (LIF), integrin β3 (ITG-β3),angiopoietin-1 (ANG-1), and CD34 protein in uterine tissue were all decreased (P<0.01). Endometrial thickness and numbers of glands and blood vessels were increased in the GY and SS groups compared with the MOD group (P<0.01), while serum IL-1β was decreased (P<0.05), E2 and PROG were increased (P<0.05), and serum interleukin 10 (IL-10) was increased in the SS group (P<0.05). Ki67, PCNA, LIF, and ITG-β3 were all increased in both treatment groups compared with the MOD group (P<0.01). PCNA was higher in the GY group compared with the SS group (P<0.05), while LIF and ITG-β3 were higher in the SS group compared with the GY group (P<0.01, P<0.05, respectively). CD34 and VEGFA levels were increased in the two treatment groups compared with the model group (P<0.01). ANG-1 was higher in the GY group than that in the SS group (P<0.01), while CD34 was higher in the SS group than that in the GY group (P<0.05). Conclusions Moxibustion at the Guanyuan and Shenshu points could help to repair the pathological thin endometrium in rats. The GY group may be superior to the SS group for reducing the levels of serum IL-1β , increasing E2, and promoting the expression of proliferation factors, while the SS group may be superior to the GY group for increasing the levels of PROG and promoting the expression of endometrium receptor-related factors. Both acupoints can promote the expression of angiogenesis factors, potentially acting via different pathways.