Phosphogypsum (PG) and titanium gypsum (TG), as a by-product (solid waste) in phosphate fertilizer and titanium dioxide industry, are causing serious environmental hazards. The resource/harmless application of PG and TG is the development trend in the future. The biological function of red yeast (Rho: Rhodotorula mucilaginosa) can effectively reduce the concentration of pollutants in the environment and has the potential of biological flotation/purification of mineral solid waste. In this study, the bioremediation mechanism and safe utilization efficiency of Rho for different contents of PG and TG were explored by using its biological flotation function. The X-ray fluorescence spectrometry (XRF) results showed that F was the main toxic element in PG and TG, and Pb and Cd did not reach the detection limit. The processing capacity of Rho for PG (>10 g/ml) is higher than that of TG (<5 g/ml). After bioleaching by Rho, the proportion of F in PG and TG solid decreased by 61.45–63.79% and 49.45–59.19%, respectively. The results of three-dimensional fluorescence, extracellular polymeric substance (EPS) extraction, X-ray diffraction (XRD), and scanning electron microscopy (SEM) confirmed that Rho could accelerate the release of harmful elements (F) in PG and TG. SEM showed that Rho cells and secretions adhered and wrapped on PG/TG, causing PG/TG decomposition and fragmentation. In addition, the adsorption of EPS and the formation of Ca5(PO4)3F are two main ways for Rho to remove F. Furthermore, under the condition of high concentration bioleaching, Rho can accelerate the release and utilization of P in PG, which is not only for the re-precipitation of Ca5(PO4)3F but also conducive to the reproduction and utilization of microorganisms. Meanwhile, the purification/safe reuse of PG by Rho is easier than that of TG. Therefore, the toxicity of PG and TG bioleaching by Rho can be greatly reduced, suggesting the huge potential of Rho in soil improvement and remediation.