We present the results of studies on the electrical and physical modifications to Poly(3-hexylthiophene), upon thermal annealing. Thermally-induced performance modifications and thermal stability of polythiophene thin film transistors are explored. We observe substantial mobility improvements in devices annealed at low temperatures (>80°C), as well as increases in on/off ratios by two orders of magnitude at moderate anneal temperatures (~120°C). We document changes in conductivity, mobility, on current, and on/off ratio with anneal temperature and total thermal budget. In conjunction with material analysis, we develop qualitative models for the mechanisms involved in the annealing/degradation processes. Hence, this study provides a comprehensive analysis of the effect of thermal cycling of polythiophene TFTs on various device performance metrics, and identifies the relevant thermal limits and failure mechanisms.