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Abstract The morphological stability of an organic photovoltaic (OPV) device is greatly affected by the dynamics of donors and acceptors occurring near the device's operational temperature. These dynamics can be quantified by the glass transition temperature (T_g) of conjugated polymers (CPs). Because flexible side chains possess much faster dynamics, the cleavage of the alkyl side chains will reduce chain dynamics, leading to a higherT_g. In this work, theT_gs for CPs are systematically studied with controlled side chain cleavage. Isothermal annealing of polythiophenes featuring thermally cleavable side chains at 140 °C, is found to remove more than 95% of alkyl side chains in 24 h, and raise the backboneT_gfrom 23 to 75 °C. Coarse grain molecular dynamics simulations are used to understand theT_gdependence on side chain cleavage. X‐ray scattering indicates that the relative degree of crystallization remains constantduring isothermal annealing process. The effective conjugation length is not influenced by thermal cleavage; however, the density of chromophore is doubled after the complete removal of alkyl side chains. The combined effect of enhancingT_gand conserving crystalline structures during the thermal cleavage process can provide a pathway to improving the stability of optoelectronic properties in future OPV devices.