Polystyrene microspheres with uniform sizes have a wide range of applications in biomedical engineering. However, detailed and systematic investigations on the influence of water content on alcohol/water systems are relatively scarce. In this study, the impact of trace water content on microsphere size was comprehensively examined, and a systematic exploration of the varying effects of different hydration levels on particle nucleation and growth mechanisms was conducted. When the water content increased from 0.1% to 0.4%, the microsphere diameter rapidly decreases from 3.6 to 2.71 μm. Correspondingly, the molecular weight increased from 29,797 to 69,186. However, within the water content range of 0.5%–14.5%, alterations in water content induced only slight variations in the microsphere diameter. The microsphere size, molecular weight, conversion rate, and reaction rate were compared in two stages. It was observed that the diminishing influence of water on the system was due to the changes in the main polymerization sites. Subsequently, the addition of water content up to 33.5% revealed an exponential decrease in the microsphere size with increasing water content in ethanol. This pattern was also observed in methanol and isopropanol, demonstrating its universality and predictability, making it applicable for precise prediction of microsphere size in different solvents.