Abstract: It is a global fact that the mineral ores degrade to the poor grade status and the various properties of ores are adversely altered such as fine dissemination and complex composition due to the continuous exploitation and utilization of phosphate rock resources. Consequently, separation of minerals has become a difficult and daunting task. The automatic mineral identification and characterization system (AMICS) is mostly used only for mineral characterization. There is no much research and literature on process mineralogy that integrates research parameters with flotation test results to quantitatively explore the mechanism of difficulties or problems faced during mineral separation. In this paper, to further explore and analyze the specific reasons for difficult problems faced while separating collophanite, a systematic in-depth mineralogical analysis based on the chemical analyses, X-ray diffraction, and AMICS has been performed on a refractory collophane flotation feed sample from Yunnan, China. The results show that the phosphorus in the sample mainly exists in the form of fluorapatite and also present in the gangue minerals, which are primarily dolomite and quartz. Fluorapatite has a fine dissemination particle size, which is in the range of 10–75 μm with a degree of mineral liberation 59.17%. Apart from existing in the form of liberated particles, fluorapatite is also present in dolomite and quartz as a composite particle and the mass fraction of composition in dolomite and quartz is found to be 26.23% and 9.92%, respectively. Further, dolomite and quartz relatively have a low degree of mineral liberation with the liberation degree of 46.82% and 39.10%, respectively. The closed-circuit flotation test was carried out with a rougher flotation to remove magnesium. Further a roughing and two stages of scavenging is performed which obtained the flotation performance of concentrate P₂O₅ grade of 29.75%, P₂O₅ recovery of 81.95%, and SiO₂ grade of 12.63%. When the results were studied together with the mineralogical analysis results, it is found that the fine dissemination particle size of collophanite, the poor degree of mineral liberation, and the serious slime generation are the main causes for not able to achieving a better performance in separation of minerals.