Casein phosphopeptide (CPP) has been widely used as micronutrient supplementation for certain populations. However, its solubility performance is far from satisfying. In this work, instant CPP powders with micropore structures were fabricated by supercritical fluid-assisted atomization (SAA) using supercritical CO2 fluid (SC-CO2) as an atomizing agent. The effects of the processing parameters (temperature, time, and pressure) on SC-CO2 absorption rate and dissolution rate were systematically evaluated and studied. The viscosity of the CPP solution increased with increased pressure of SC-CO2 as pressure increased its solubility. The processing conditions are optimized as follows: 40 °C, 40 min, and 8.27 MPa, with an SC-CO2 absorption rate of about 8 wt.%. The dissolution time of the SAA-CPP powders was significantly decreased from 1800 s to 54 s at room temperature, due to the micropore structures and almost 10 times increase in the specific surface area of SAA-CPP. The bioactivities of the instant SAA-CPP, especially the calcium-binding capacity, were also evaluated and showed no observable difference. Among the four CPPs prepared in different ways in this work, SAA-CPP had better dissolution performance. The results show that SAA technology is a promising way to prepare instant polypeptide powders.