The carrier mobility of poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) semiconductors can be substantially enhanced after heating through a thermotropic mesophase transition, which causes a significant improvement in thin film structural order. By directly measuring film structure throughout a heating and cooling cycle, we identify the molecular origin of this mesophase transition as the melting of interdigitated linear alkane side chains, in this case quaterdecyl. The morphology and phase behavior throughout the thermal cycle are controlled by the changing conformation of the side chains. Surprisingly, the melting of the side chains allows increases in the backbone order, pi-pi stacking, and carrier mobility. Upon cooling, the side chains recrystallize to preserve the excellent mesophase order and enhanced electrical performance.