In the previous work, we have reported that small dosages of the polymethylsilsesquioxane (PMSQ) microsphere can effectively improve the performance of the EVA pour point depressant (PPD) and the amount of EVA PPD adsorbed on the microsphere evidently influences the efficiency of the EVA/PMSQ composite particle. To further promote the adsorption of EVA on the microsphere and enhance the efficiency of the composite particle, here, the amino-functionalized PMSQ microspheres with different amino molar ratios (PAMSQ) are first synthesized and characterized. The flow behavior, exothermic crystallization and microstructure of the waxy crude oil undoped/doped with EVA, EVA/PMSQ and EVA/PAMSQ are systemically investigated. Results show that 50 ppm EVA PPD can greatly improve the flow behavior of the oil and small dosages (2.5 ppm) of PMSQ microsphere can significantly improve the performance of the EVA PPD. After the amino-functionalization, the flow improving efficiency of EVA/PAMSQ is further enhanced: the gelation point, G', G'', apparent viscosity and yield stress of the oil sample decrease to a lower value. The best performance is found at adding 50 ppm EVA + 2.5 ppm PAMSQ-2 (with amino molar ratios at 15%). Compared to EVA/PMSQ, the EVA/PAMSQ exhibits a stronger nucleation effect to increase the WAT of the oil sample slightly, and outstandingly modifies the morphology of the precipitated wax crystals into larger and more compact flocs. The amino-functionalization facilitates more EVA PPDs adsorbing and concentrating on the PAMSQ microsphere, causing the formation of the EVA/PAMSQ composite particles. The composite particles provide stronger nucleation effect for the wax precipitation, resulting in larger and more compact wax microstructures and then further improving the flow behavior of the oil. The rheological improving performance of EVA/PAMSQ for the waxy crude oil increases with the increase of amino molar ratio and the efficiency of EVA/PAMSQ-2 reaches the best. When the amino molar ratio is too high (PMASQ-3), the PAMSQ-3 microsphere is unstable in oil phase and aggregates into large particle flocs, which inhibits the EVA adsorption on the PAMSQ-3 microsphere and then weakens the rheological improving efficiency of the EVA/PAMSQ-3 composite particle.