The crystallization and aggregation behaviors of semiconducting polymers play a critical role in determining the ultimate performance of optoelectronic devices based on these materials. Due to the soft nature of polymers, crystallite imperfection exists ubiquitously. To this aspect, crystallinity is often used to represent the degree of crystallite imperfection in a reciprocal relation. Despite of the importance, the discussion on crystallinity is still on the phenomenological level and ambiguous in many cases. As two major contributors to crystallite imperfection, crystallite size and paracrystallinity are highly intertwined and hardly separated, hindering more accurate and trustworthy structural analysis. Herein, with the aid of synchrotron-based X-ray diffraction, combined with environmentally controlled heating capability, the evolution of crystallite size and paracrystallinity of two prototypical polythiophene-based thin films have been successfully measured. Strikingly, the paracrystallinity of poly(3-hexylthiophene-2,5-diyl) (P3HT) crystallites remains unchanged with annealing, while the paracrystallinity of poly[2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT) becomes diminished with crystallite growth. This work delivers a promising gesture to semiconducting polymers community, confirming that it is possible to experimentally separate crystallite size and paracrystallinity, both of which are highly intertwined. With this progress, investigation on the correlation between further detailed microstructural parameters and device performance can be achieved.