Background. We attempt to discuss the function of self-made prescription compound Rhodiola rosea on the kidneys of rats with type 2 diabetic nephropathy (DN), through studying the effects of self-made rescription compound Rhodiola rosea on the ultrastructure of podocytes in rats with DN. Methods. DN rat model was established by streptozotocin. The successfully modeled rats were divided into 4 groups, DN group, compound Rhodiola low-dose group, medium-dose group, and high-dose group. Compound Rhodiola low-dose group, medium-dose group, and high-dose group were administered for 8 weeks, and the DN group and the blank control group were administered with normal saline. The podocyte count, podocyte width, podocyte fusion rate, and average thickness of glomerular basement membrane were compared in each group, and the ultrastructural changes in podocytes were observed by transmission electron microscope. Results. Compared with the normal control group, the number of podocytes in the DN group remarkably reduced, but the width level of podocyte, the fusion rate of podocyte, and the average thickness of basilar membrane remarkably increased (
P
<
0.05
). Compared with the DN group, the number of podocytes in the high-, medium-, and low-dose groups increased remarkably, but the width level of podocyte, the fusion rate of podocyte, and the average thickness of basilar membrane decreased remarkably (
P
<
0.05
). Compared with the low-dose group, the number of podocytes in the high-dose group and the medium-dose group increased remarkably, but the width of podocyte, the fusion rate of podocyte, as well as the average thickness of basilar membrane remarkably reduced (
P
<
0.05
). Various indicators of high- and medium-dose groups had no statistical difference (
P
>
0.05
). Conclusions. Self-made prescription compound Rhodiola rosea can promote the recovery of podocyte in DN rat and protect their kidney.