Abstract: Given the scarcity research on the activation of selenium (Se) by organic acids in acidic soils, a pot experiment was conducted to investigate the effects of different amounts of exogenous compound organic acids (COA) on the uptake and transport of Se in rice as well as soil properties under acidic soil conditions, providing technical support for the production of Se-enriched rice. This study consisted of four treatments: 0 COA (CK), 0.23 mg∙kg^–1 COA (LOA), 1.14 mg∙kg^–1 COA (MOA), and 2.28 mg∙kg^–1 COA (HOA). The results showed no significant difference in grain yield or aboveground biomass of rice between CK and COA treatments under the equal application of Se 0.5 mg(Se)∙kg^–1. However, LOA and MOA treatments significantly increased the Se content in rice grains by 28.7% and 27.3% and the accumulative amount of Se in the whole plant by 40.1% and 34.1%, respectively, compared with CK. In contrast, the HOA treatment significantly decreased the Se content and accumulation in rice stems compared with CK, with reductions of 23.5% and 46.7%, respectively. The data indicated that the LOA and MOA treatments effectively enhanced Se uptake and transport, while the HOA treatment inhibited the transport of Se from the roots to stems. Additionally, the COA treatments significantly increased the available phosphorus content in the rhizosphere soil and the available Se content in the non-rhizosphere soil, decreased the available sulfur content in both the rhizosphere and non-rhizosphere soils, and enhanced the activities of catalase (CAT) and peroxidase (POD) in the roots. Particularly, the MOA treatment significantly increased soil urease activity (UE). The LOA treatment reduced the dissolution effect of root activities on kaolinite minerals, while the HOA treatment exerted a promoting effect. Principal component analysis indicated that soil UE activity and root CAT activity made significant contributions to the uptake and accumulation of Se in plants. In conclusion, exogenous addition of 0.23–1.14 mg∙kg^–1 COA can improve the availability of soil Se, enhance the activities of CAT and POD in rice roots, and significantly increase the Se content in various parts of rice (2.52–8.56 mg∙kg^–1) and the Se accumulation in plants (177.2–185.2 μg∙plant^–1). This study provides new ideas and approaches for enhancing the Se content in rice grains and has important theoretical and practical significance for meeting the human need for Se.