A series of polyimide films were synthesized based on various side-chained diamines, 4-phenylphenyl-3,5-diaminobenzoate (DABB), 6-(4-phenylphenoxy)hexyl-3,5-diaminobenzoate (C6BB), 6-(4-(4-butoxylphenyl)phenoxy)hexyl-3,5-diaminobenzoate (C6BBC4) and 4-(4-butoxylphenyl-phenyl-3,5-diaminobenzoate (BBC4), the side chains of which contain a rigid biphenyl linked with flexible alkyl. The pretilt angle of liquid crystal molecules on the side-chained polyimide films based on C6BBC4 or BBC4 (PI-C6BBC4 or PI-BBC4) increased obviously with increasing side chain content and even achieved 87–89°. In contrast, the polyimide film based on C6BB or BB (PI-C6BB or PI-BB) even with a high side chain content could only achieve the homogeneous alignment. The properties and microscopic structure of the functionalized polyimide films were analyzed by polarized ATR-FTIR, computer simulations and surface energy etc. It was found that the side chains with different chemical structure get the different orientation and conformation in the outmost layer of polymer film, affecting the pretilt angle of liquid crystal molecules on this film surface. For PI-BBC4 and PI-C6BBC4, the side chains with the non-polar group at the tail take the vertical conformation in the outer layer of the polymer surface, which benefited the liquid crystal to get a large pretilt angle, even vertical alignment on the film surface. The side chain of PI-C6BB with the flexible alkyl spacer is equipped with good mobility. It is easy for its polar mesogen groups at the surface to take the conformation parallel to the polymer film, which leads to the formation of homogeneous alignment of LC molecules.