Control of molecular alignment in liquid-crystalline polymer films plays an important role in the development of highly functional materials. A photoalignment method has drawn much attention due to its clean and non-contact process. Recently, we have proposed a novel photoalignment method termed scanning wave photopolymerization (SWaP), where photopolymerization with scanned light triggers molecular diffusion and alignment. In this method, molecular alignment proceeds simultaneously with polymerization and crosslinking reactions; thus, these reactions would affect the alignment behavior. In this study, we investigated the effect of crosslinkers and polymerizable functional groups on the alignment behavior. Furthermore, we evaluated the thermal stability of molecular alignment in the polymer films fabricated by SWaP of monomers with different polymerizable functional groups.