In this work, GJBW, a fatty acid‐based agent, was used as an efficient collector to separate dolomite from apatite to achieve high‐purity apatite. The flotation performance of dolomite and apatite in the phosphate (H3PO4) system treated with sodium oleate (NaOl) and GJBW, respectively, was studied and compared. Microheat tests, surface characterization, and flotation solution chemistry calculations were used to evaluate the adsorption mechanism of GJBW onto dolomite. The smoothness and flatness of dolomite treated and untreated with GJBW may be also detected via atomic force microscopy (AFM). Microflotation results illustrated that GJBW performed better than NaOl for separating apatite from dolomite under the H3PO4 system. The grade of P2O5 in concentrates treated with 10 mg/L GJBW was 31.49%, which was 4.98% higher than that of NaOl. The recovery rate of P2O5 was 87.05%, which was 4.71% higher than that of NaOl. Microheat tests demonstrated that GJBW generated a higher heat of adsorption onto dolomite than did the same concentration of NaOl, significantly enhancing the dolomite's hydrophobicity. Fourier transform infrared spectroscopy (FTIR), zeta potential, flotation solution chemistry calculations, and surface characterization further demonstrated that GJBW may ionize large amounts of RCOO− and H (RCOO)2− ions in solution, which can be significantly chemisorbed with numerous sites of Ca and Mg exposed to dolomite, forming dense point‐like adsorption onto dolomite. These findings shed more light on the mechanism of interaction between GJBW and dolomite, which has profound implications for the study and use of fatty acid‐based treatments in phosphate ores.