Despite the wide industrial application of poly(tetrafluoroethylene-co-perfluoroalkylvinyl ether) (PFA) in semiconductor processing, its crystallization behavior has little been studied. In this work, three PFA resins with similar molecular weight but different comonomer content and distribution were synthetized. Then the non-isothermal crystallization kinetics and crystalline structures were studied by differential scanning calorimetry, polarizing optical microscopy, and X-ray diffraction systematically. It is found that the incorporation of comonomers destroys the chain regularity and reduces the crystallizability of PFA thermodynamically, while the comonomer insertion improves the chain flexibility to accelerate the crystal growth dynamically. When the comonomer content of PFA is low, both the nucleation and growth rates are quite fast, which is favorable for the formation of spherulite. As the comonomer content increases or distribute uniformly in the chain, the nucleation rate declines notably and the side groups distort the crystal cell to increase the spacing of [100] plane. Moreover, two-dimensional growth mode is dominant to form bundle-like structure when crystallizing at slow cooling, where nucleation is suppressed by growth. But three-dimensional symmetrical spherulite can be activated and perfected at high cooling rate due to the initiation of substantial nucleation sites. This unique crystallization behavior is opposite to that of conventional polymers, providing a guidance for the polymerization and processing of PFA.