Numerous minerals found in nature contain silica, including quartz, cristobalite, opal, etc. They have the same chemical composition but different crystal structures, and this phenomenon is called “polymorphism” in mineralogy. For these polymorphic and multi-like minerals, in the flotation process, will it directly or indirectly affect the flotation effect. Based on this, this study mainly explores the difference between crystalline SiO₂ and amorphous SiO₂ in flotation. In this study, two crystal forms of SiO₂ were subjected to flotation and adsorption capacity tests. FTIR, other test techniques, the chemical calculation of the flotation solution, and the theoretical calculation of the DLVO can all be used to provide an explanation. Finally, in the flotation experiment, the feedbacks of the two minerals to the change of the pH value of the pulp and the change of the concentration of the reagent are different. Through the comprehensive analysis of the adsorption capacity test and semi-quantitative calculation of the infrared spectrum, the adsorption capacity of crystalline SiO₂ to drugs is about 23% higher than amorphous SiO₂. Furthermore, during the flotation process, the amorphous SiO₂ particles will agglomerate together and entrain into the foam through, resulting in concentrate pollution. So amorphous SiO₂ will undoubtedly increase the difficulty of flotation.