A series of branched poly(ethyleneimine) (PEI) derived polymers with different lengths of n-alkyl side chains, denoted as PEI(n)Cs (n = 12, 14, 16, 18, 20, number of carbon atoms in alkyl side group), have been prepared by a N-alkylation method, and systematically characterized by differential scanning calorimertry (DSC) and wide-angle X-ray diffraction (WAXD) as well as Fourier transform infrared spectroscopy (FTIR). The side chains grafted on these comblike polymers are long enough to form crystalline phase composed of paraffin-like crystallites. The crystallization of the side chains forces the branched poly(ethyleneimine) molecules to pack into layered structure, between which the crystallites are located. The melting temperatures of the side chain crystallites increase from −12.36 to +51.49 °C with increasing the length of the side chains from n = 12 to n = 20, which are a little bit lower than the corresponding pristine n-alkanes. PEI18C was taken as an example in this work for the investigation of phase transition and conformational variation of the side chains with temperature changing. With temperature increasing, the crystalline phase of the side chains undergoes a phase transition process from orthorhombic to hexagonal form and then from hexagonal to melt state. Similarly, increasing temperature leads to the regular trans sequences of the orthorhombic phase transforming to conformationally disordered trans sequences of the hexagonal phase and then to the gauche conformational state (melt state) at higher temperature. The above-described experimental phenomena for both crystalline transition and conformational structure variation are reversible as temperature decreases. Combining the transformations of the crystalline phase and the conformational structure, it is confirmed that hexagonal phase exists as an intermediate phase in the process of temperature variation.