A series of donor-acceptor type of π-conjugated copolymers based on tert-butoxycarbonyl (t-Boc) substituted indigo, isoindigo or diketopyrrolopyrrole as the acceptor unit and a benzodithiophene derivative as the donor unit was designed and synthesized. These copolymers can be readily dissolved in organic solvents and can produce uniform films by solution deposition. Thermal treatment of copolymer films at elevated temperature resulted in elimination of t-Boc side groups in nearly quantitative yield as suggested by thermogravimetric analysis and fourier transform infrared spectroscopy. The elimination of the bulky t-Boc side groups resulted in the emergence of hydrogen bonding interactions by virtue of the lactam structures of the indigo, isoindigo and diketopyrrolopyrrole units. Of particular interests is the distinctly increased field-effect mobility of these copolymers after thermal treatment, which may arise from the enhanced coplanarity and intermolecular ordering of the indigo, isoindigo or diketopyrrolopyrrole units after elimination of the bulky t-Boc side groups. These results demonstrate that the incorporation of latent side groups provides a viable strategy to construct conjugated polymers that can attain more ordered intermolecular stacking by simple thermal treatments.