This study investigates the influence of various factors on shear flocculation in the apatite-dolomite mixed ore flotation system. The Box-Behnken response surface methodology is employed to evaluate the interactions of these factors on flocculation behavior. Additionally, the Focused Beam Reflectance Measurement (FBRM) and Particle Vision Measurement (PVM) techniques are applied to investigate the mechanisms by which these factors affect shear flocculation. The results show that sodium oleate (NaOL) concentration, pH, and shear rate significantly influence the size of the flocculated particles. Notably, the interaction effect between NaOL concentration and pH is particularly pronounced. FBRM and PVM analysis reveals that pH and NaOL concentration play dominant roles in controlling particle flocculation, while H3PO4 has a relatively minor impact on agglomerate morphology and size. At low shear rates, the flocs are larger and more uniformly distributed, resulting in a more stable process. In contrast, although high shear rates enhance initial flocculation efficiency, they reduce floc size. Furthermore, the modified Smoluchowski model is applied to evaluate the impact of different factors on flocculation kinetics. The findings suggest that the effects of these factors vary across different stages of flocculation. The combined influence of NaOL concentration, pH, and shear rate is crucial in determining the stability of the flocs, with these three factors being key determinants of floc morphology and stability.