Reproductive failure in cotton caused by drought has been reported to be closely associated with alterations in pistil fertility; however, the mechanism of the effect of drought on pistil fertility in cotton is less studied. We hypothesized that drought would inhibit the ovule formation to alter pistil potential fertility. To address this hypothesis, we conducted a water deficit induction experiment with a cotton cultivar, Dexiamian 1. Results showed that drought damaged the cytological structure of the developing ovules. This resulted in a lower ovule number, finally leading to lower cottonseed number and boll weight. And the decreased ovule number was closely related to the reactive oxygen species (ROS) accumulation in pistil during ovule development. Further analysis of antioxidant metabolism found that in the enzymatic antioxidant system, drought decreased the activities of superoxide dismutase (SOD) and catalase (CAT), resulting in the accumulation of superoxide anion () and hydrogen peroxide (H2O2). Regarding the non‐enzymatic antioxidant system, the elevated glutathione reductase gene (GhGR) expression under drought promoted the glutathione (GSH) accumulation; however, the decreased dehydroascorbate reductase gene (GhDHAR2) expression under drought inhibited the conversion of GSH to ascorbic acid (AsA). Although the increased monodehydroascorbate reductase gene (GhMDHAR) expression under drought promoted AsA accumulation, drought‐induced reduced ascorbate peroxidase gene (GhAPX) expression inhibited the reduction of H2O2 by AsA, which ultimately led to higher AsA content and H2O2 content. We conclude that drought impedes the ovule formation by disturbing pistil's antioxidant metabolic homeostasis to destruct the cytological structure of the developing ovules.