In this study, soybean germination was investigated by using the uniform table of U10 (103) with the function of disclosing the interactive correlation of different factors. The enrichment of three human essential trace elements, Zn, Co, and Se, was carried out during the germination of soybean and growth of soybean sprouts. The amounts of enriched zinc, Co and Se and their amounts after organic enrichment were evaluated, and the regression relationships between the amounts of exogenous zinc, Co and Se after bioaccumulation and the exogenous concentrations of zinc, Co and Se in different treatments were examined. The interactions of exogenous concentrations of Zn, Co and Se with their enrichment as well as the enrichment trends of Zn, Co and Se were found. The results showed that the interactions took place in the late stage of sprout growth (after 30 h), and the interactions of [Zn×Co] and [Co×Se] were synergic. The absorption of Zn by sprouts was promoted through double synergic effects of the exogenous Se, and antagonism was found between [Zn×Se] and [Zn×Co×Se]. The absorption of Se by sprouts was inhibited through double antagonistic effects of the exogenous Zn. The organic conversion rates of the elements were low at the early stage of sprout growth (for the first 30 h), with the enrichment of the elements mainly via physical dialysis and absorption. In the late stage of sprout growth (after 30 h), organic enrichment took place through the interactions of exogenous concentrations of the elements. The comprehensive evaluation revealed that the 3rd, 6th and 9th treatments were particularly effective for simultaneous enrichment of Zn, Co and Se in the sprouts, especially with the 3rd treatment (Zn2+-Co2+ mixture: [Zn2+]=1200 μg/L, [Co2+] =30 μg/L; Se4+ solution: [Se4+]=180 μg/L) applied for 45 h (which led to the optimized enrichment of Zn, Co and Se: Zn2+=8.58 mg/kg, Co2+=63.10 μg/kg, Se4+=48.30 μg/kg). The organic conversion rates of Zn, Co and Se were 49.50%, 25.94%, and 56.25%, respectively. The total amounts of the three enriched elements all essentially reached their recommended intakes indicated by the Chinese dietary guidelines. The obtained results provide references for the production of healthy vegetables enriched with multiple elements like Zn, Co and Se.