The performance of polymer field effect transistors (FETs) can vary by orders of magnitude by applying different processing conditions. Although it is generally believed that a higher degree of crystallinity results in a higher mobility, the correlation is not straightforward. In addition, the effect of cross-linking on polymer thin film microstructural order is relatively unknown. This study investigates the effect of thermal annealing and UV-initiated photo-cross-linking on the FET performance and microstructural order of a photo-cross-linkable P3HT derivative. Our results demonstrate that while cross-linking did not disrupt the overall crystallinity of the polymer thin film, the photo-cross-linking process likely induced doping in the semiconductor layer, leading to the absence of saturation behavior in the FET. Annealing after cross-linking slightly improved the FET performance but only minimally affected the microstructural order of the polymer film since the 3D morphology had been "locked in" during the first cross-linking step. Importantly, annealing and cross-linking simultaneously was a successful method to preserve polymer crystallinity while also achieving effective cross-linking. Using newly developed quantitative X-ray analysis techniques, our study established a quantitative correlation between FET charge mobility and thin film crystallinity.