In highly variable estuarine environments, short-lived fishes must balance immediate reproduction against future growth, yet the reproductive role of maternal size remains poorly resolved. Here, we analyzed biological surveys of the yellowfin goby Acanthogobius flavimanus from Haizhou Bay, Yellow Sea, collected between 2023 and 2025, combining fecundity estimation, egg morphometry, histology, and size-structured reproductive-output modeling. Absolute fecundity scaled hyperallometrically with total length (β = 3.18, 95% CI: 3.05–3.31, R² = 0.71, p < 0.001), while mean egg diameter increased significantly with maternal size (R² = 0.65, p < 0.001), yielding an approximately 3.15-fold increase in estimated egg volume across the observed size range. Histology revealed contrasting ovarian developmental phenotypes within the same spring cohort: a precocious phenotype with active vitellogenesis and a delayed-development phenotype with structurally intact early-stage oocytes and higher condition factor. Relative Reproductive Output (RRO) modeling showed that females > 180 mm total length represented only 4.8% of abundance but contributed 18.5% of total standardized egg-production output under the assumptions of the model. Inter-annual monitoring further indicated a decline in mean body size and in the proportion of large individuals from 2023 to 2025, a pattern consistent with size truncation but requiring longer-term monitoring for causal attribution. These findings suggest that large females can contribute disproportionately to reproductive output even in a short-lived estuarine fish and support the inclusion of size structure in fisheries assessment and management.