To address the contradiction between the widespread prevalence of selenium deficiency and the growing demand for selenium-enriched fruits, this study utilized phosphate tailings (industrial solid waste), wood vinegar (a by-product of forestry processing), biochemical fulvic acid, and alginic acid (renewable biomass resources) to construct an organic–inorganic composite soil selenium activator. This formulation enhances the mobilization of inherent selenium in the soil without relying on exogenous selenium supplementation, thereby improving selenium bioavailability while mitigating the environmental pollution and resource depletion associated with external selenium inputs. Through field experiments, we systematically evaluated the influence of varying activator dosages on soil physicochemical properties, available selenium content, selenium distribution in different citrus organs, and fruit quality. The results demonstrated that the application of the compound activator at 600 g/plant significantly increased (p < 0.05) soil available selenium and fruit selenium content by 21.26% and 21.06%, respectively. During the fruit expansion stage of Sugar Orange, soil available selenium was elevated by 21.8%, which corresponded to a 21.09% increase in fruit selenium content. Regarding fruit quality parameters, Sugar Orange exhibited increases in soluble solids (35.8%), citric acid (20.3%), solid-to-acid ratio (77.8%), and selenium content (223.3%). In Rock Sugar Orange, significant enhancements were observed in soluble solids (46.1%), vitamin C (45.3%), total soluble sugars (73.4%), solid-to-acid ratio (156.6%), and selenium content (69.7%). Structural equation modeling revealed that soil available selenium, soil properties, and selenium content in citrus organs collectively exerted positive regulatory effects on fruit quality. Specifically, juice selenium content showed significant positive correlations with fruit shape index, individual fruit weight, soluble solids content, and solid-to-acid ratio. This strategy achieves the synergistic reuse of industrial solid waste and agricultural biomass resources, offering a green and sustainable pathway to enhance selenium content and quality in citrus fruits.