In this work, we report on the thermally induced phase behavior and crystalline structures of a series of solution-processable naphthalene diimide (NDI)-based molecules with alkyl side chains of varying length and branching. Taking advantage of synchrotron-based in situ grazing-incidence wide-angle x-ray scattering, the most kinetically favorable thin film crystalline structures of each molecule at room temperature and at elevated temperatures were resolved. The extracted unit cell parameters of the kinetically favorable crystal structures as a function of temperature were used to quantify the anisotropic thermal expansion coefficients along the three principal crystallographic directions. In particular, it is found that long alkyl side chains can effectively suppress crystalline polymorphism and enhance thermal reversibility. The acquired knowledge regarding the thermally induced phase transitions of thin films based on NDI-based small molecules with varying solubilizing side chains serves as guidance for further molecular design and synthesis of high performance n-type small molecules.