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The uterus is a pivotal organ for mammalian reproduction, directly determining reproductive success by orchestrating embryo implantation, placental development, fetal nourishment, and parturition. However, the molecular mechanisms regulating high fecundity in the uterus across different stages of the estrous cycle remain unclear. This study aimed to elucidate the genetic regulation of goat fecundity through integrated proteomic and transcriptomic analyses of uterine tissues. Twenty healthy female Yunshang black goats (2–3 years old, body weight 52.22 ± 0.43 kg) were stratified into high- and low-fecundity groups during the follicular (FH and FL, n = 5 per group) and luteal (LH and LL, n = 5 per group) phases. Using data-independent acquisition (DIA) mass spectrometry, we quantified 4,455 proteins. Weighted gene co-expression network analysis (WGCNA) identified the lightcyan module as highly correlated with high fecundity in the luteal phase, with hub proteins including IDH2, PSAT1, MDH1, UBQLN1, RPLP1, SEC23B, RAD23B, PSPH, and MTHFD2. Additionally, 125 and 183 differentially abundant proteins (DAPs) were detected in the FH vs. FL and LH vs. LL comparisons, respectively. Biological adhesion processes, closely linked to transport activity, were implicated in uterine function, with key proteins such as PKP4, COL4A1, LPCAT4, ARRB1, SERPINA5, CDK9, and HDAC7 identified as potentially critical for embryo–uterine communication. Integrated transcriptomic and proteomic analyses revealed significant upregulation of the relaxin signaling pathway during the follicular phase, which may promote uterine tissue remodeling, extracellular matrix degradation, and angiogenesis, thereby facilitating preparation for embryo implantation. During the luteal phase, enhanced activity of the terpenoid backbone biosynthesis pathway was observed, which may indicate an increase in the production of cholesterol and steroid hormone precursors, potentially supporting metabolic demands and pre-receptive steroid signaling in the uterus. Our findings demonstrate that specific protein co-expression modules and hub proteins are closely associated with high fecundity in goats. The stage-specific activation of key pathways, including relaxin signaling and terpenoid backbone biosynthesis, may reflect dynamic molecular reprogramming of the uterus during the estrous cycle. This study provides insights into the molecular mechanisms underlying uterine prolificacy in Yunshang Black goats. However, these findings are based on proteomic and transcriptomic data, and further experimental validation is needed to confirm the causal relationships.