Polymer microspheres can be used as fuel containers for laser inertial confinement fusion (ICF) due to their low atomic number, low density, and high thermal stability. The thin-walled polymer microspheres are prone to cracking due to an increase in the diameter to thickness ratio (diameter/wall thickness).The effect of polystyrene (PS) and Poly (α-methyl styrene) (PAMS) materials commonly used in ICF experiments on the quality of thin-walled microspheres is investigated. PS hollow microspheres show better sphericity, smoother surface, and lower cracking rate than PAMS microspheres. Moreover, the heat treatment of solidified PS microspheres can improve the strength so that the cracking rate of the microspheres decreases. The relative mechanism of how the molecular structure affect the quality is also discussed. This study provides some guidance for the preparation of thin-walled polymer microspheres with high quality for ICF experiments.