Paeonia ludlowii (Stern & Taylor) D.Y.Hong, an endangered species, is indigenous to Tibet, China and propagated only by seed under natural conditions. Its natural reproduction is constrained by low fecundity. Excess seed abortion is a key factor restricting its natural reproduction, cultivation, introduction, and protection. Understanding the specific origin and occurrence of aborted ovules is important for the protection of offspring. Using serial sectioning analysis, we studied the process of pollination and fertilization of P. ludlowii and examined the characteristics of aborted ovules, developmental differences after flowering of normal and aborted ovules, and their ratios at different positions in P. ludlowii ovaries. During pollination, fertilization, and seed development, ovule abortion was frequent, with a random abortion position. There were three types of abortion, namely, abnormal pistil, sterile ovules, and embryo and endosperm abortions. Of these, embryo and endosperm abortions could be divided into early abortion and middle abortion. The early aborted ovules stopped growing on day 12, the endoblast and endosperm in the embryo sac aborted gradually. Furthermore, the shape of the embryo sac cavity changed. The volume of aborted ovules was significantly different from that of fertile ovules. At ripening, the external morphology of different types of aborted seeds was significantly different. The possible reasons for the abortion of the ovules are also discussed.