Soil acidification has become an increasingly serious problem. Due to aluminum toxicity and phosphorus deficiency, the root development of many crops is hindered. In this study, we aimed to investigate the mechanism involved in aluminum toxicity and reduction of phosphorus absorption under acidic conditions using Saccharomyces cerevisiae as a model organism. The high-affinity phosphate transporter PHO84 was sensitive to aluminum under low-phosphorus conditions, and the addition of phosphate alleviated this sensitivity. The reduction of phosphate absorption induced by aluminum is dependent on PHO84. The sensitivity assay of corresponding gene mutations in the phosphate signaling transduction pathway indicated that the effect of aluminum on PHO84 is related to the phosphate signaling transduction pathway system and regulated by PHO4/PHO2; however, aluminum did not affect the pho84p transport mediated by Pho86p through the sensitivity detection of pho86Δ to aluminum. Our results corroborate the finding that aluminum reduces phosphorus absorption and inhibits the growth of the plant in acidic media. Additionally, the high-affinity phosphate transporter NtPT1 in tobacco exhibits a similar role to PHO84 in yeast cells, indicating that the reduction of phosphorus absorption caused by aluminum depends on NtPT1 in tobacco. Altogether, our results may provide basis for the engineering of aluminum-resistant microorganisms or plants and the treatment of acidic soil.