With high-grade apatite resources exhausted and economic development, enhancing the apatite quality from calcium gangue such as dolomite has a great significance for production. However, it is difficult to separate apatite from dolomite effectively due to the similar surface properties. In this study, the N-carboxybutyl chitosan (CBC) was tested as a potential selective depressant to separate apatite from dolomite in the sodium oleate (NaOL). Flotation results of single mineral and artificially mixed mineral confirmed the selective depression effect of CBC. The depression mechanism of CBC was investigated using wettability analysis, Fourier Transform Infrared (FTIR), and X-ray Photoelectron Spectroscopy (XPS) analyses. The results indicated that the CBC adsorption quantity and intensity on the dolomite surface more than that on the apatite surface, which was due to CBC absorbed on apatite surface by hydrogen bonding, while absorbed on dolomite surface mainly through chemical chelating between Ca on the mineral surface and -COO- on the depressant. These adsorption differences led to the flotation separation of the two minerals.