Objectives A comparison of different administration routes of clodronate disodium liposomes to determine which is the most effective method of rat endometrial macrophage clearance. Methods Female 8-week-old SD rats were randomly divided into the unilateral control group (injected 100μL PBS liposomes into the left uterine cavity), unilateral clearance group (injected 100μL clodronate liposomes into the right uterine cavity), bilateral control group (injected 100 μL PBS liposomes into the bilateral intrauterine), bilateral clearance group (injected 100 μL clodronate liposomes into the bilateral intrauterine), and whole-body control group (injected 500 μL PBS liposomes into the caudal vein ) and whole-body clearance group (injected 500 μL clodronate liposomes into the caudal vein). Haematoxylin and eosin (H&E) staining was used to observe the morphology and structure of uterine and ovarian tissues, immunohistochemistry was used to observe the positive presence of macrophages in uterine and ovarian tissues, and flow cytometry was used to detect changes of the macrophages cell counts in uterine and ovarian tissues. Results There was no significant difference in the structure and morphology of the uterus and ovary among all groups. Immunohistochemical staining showed that compared to the control group, the positive expression of uterine macrophages in unilateral and bilateral clearance groups was significantly decreased (P<0.001), and had no effect on the accumulation of macrophages in the ovary (P>0.05). The numbers of macrophages in both uterine and ovarian tissues decreased of whole-body clearance group (P<0.01, P<0.01). Compared with unilateral and bilateral clearance groups, whole-body clearance group had a greater effect on the positive expression of macrophages in ovarian tissues (P<0.05). Flow cytometry showed that compared with the control group, the percentage of macrophages in the uterine tissue was significantly reduced in each clearance group (P<0.001, P<0.001, P<0.05). Compared to the whole-body clearance group, the clearance effect of endometrial macrophages was better in the unilateral and bilateral clearance groups (P<0.05，P<0.05). In addition, the number of macrophages in ovarian tissue decreased in all clearance groups compared to the control group. The decrease in macrophage number was most pronounced in the whole-body clearance group (P<0.05), and there was no statistically significant difference between the unilateral and bilateral clearance groups compared with the control group (P>0.05).