Ceramic aerogels prepared by the route of polymer-derived ceramics (PDCs) have been of significant attention in high-temperature insulation. However, the application of ceramic aerogels was seriously confined due to the structural damage and shrinkage cracking of ceramic precursors during pyrolysis. In this investigation, precursor ceramic microsphere aerogels with outstanding antishrinkage properties were prepared by storing strain in curled molecular chains and using polysilazane (PSZ) as the precursor. Meanwhile, precursor ceramic microsphere aerogels with different curled molecular chain structures were prepared by modulating solvent interactions and cross-linked structures. Different curled molecular chain structures were formed, and the impact on the antishrinkage properties of precursor aerogels was analyzed. The shrinkage resistance, thermal insulation, and mechanical properties of the prepared aerogels were tested and compared. Furthermore, the mechanism of the impact of different curled molecular chain structures on thermal insulation and mechanical properties was investigated through multiscale simulations combined with fractal theory. The thermal and stress transfer at the interfaces of different microsphere skeleton structures and the mechanisms were investigated. An idea for solving the problem of pyrolytic shrinkage in the preparation of ceramic aerogels was provided in this investigation. In addition, insights into the influence of the microsphere skeleton structure on the thermal and mechanical properties of ceramic aerogels were provided.