This study investigated the effects of humic acid (HA), flue gas desulfurization gypsum (FG), and their combined application on soil chemical properties, rice yield, phosphorus use efficiency (PUE), and phosphorus agronomic efficiency (PAE) during rice production in acidic paddy soil, which has not been previously studied. The greenhouse experiment was conducted in a completely randomized block design with four treatments, including a control (with no soil amendments), HA (975 kg ha− 1), FG (636 kg ha− 1), and HA combined with FG. The application of HA increased soil pH, total organic carbon (TOC), cation exchange capacity (CEC), total concentrations of P, Ca, and S, and exchangeable Ca and S. In addition, the application of HA maximized rice yield, total P uptake, PUE, and PAE. The application of FG increased the soil total Ca, whereas the coapplication of HA and FG increased TOC, CEC, available P, exchangeable Ca, exchangeable S, and total S. However, the application of FG, both alone and in combination with HA, failed to increase rice yield, PUE, and PAE owing to lower total P uptake by plants. Therefore, HA application alone is a sustainable soil management practice for acidic paddy soils. In contrast, FG application alone must be careful considered, as it resulted in disappointing agronomic effects.