We have proposed a new fabrication process of donor and acceptor charge transfer complex thin films using thermal diffusion. 2,3,5,6-Tetrafluoro-7,7,8,8-tetracyano-quinodimethane (F4-TCNQ) was vacuum-deposited on 2,7-didecylbenzothienobenzothiophene (C10-BTBT) thin films fabricated by spin-coating, and F4-TCNQ molecules were diffused into C10-BTBT thin films by thermally annealing. The X-ray diffraction pattern and field effect transistor of thermally annealed thin films indicated the crystal structure of the charge transfer complex of C10-BTBT and F4-TCNQ and n-channel operation in air, respectively. We conclude that it is good process to use the thermal diffusion for the fabrication of the large area thin films of charge transfer complex.