Topological polar structures are attracting attention as potential applications of next-generation high-density memories. We investigate how the ferroelectric domain evolves with film thickness in c-axis oriented epitaxial Bi2WO6 thin films grown on (LaAlO3)0.3(Sr2AlTaO6)0.7 substrates. In addition to the general thickness scaling effect on domain size, we find that 3- or 4-variant domains appear in a sample thicker than 120 nm, whereas ⟨100⟩-type domains compete with the ⟨110⟩ ones in thinner samples, resulting in a variety of nontrivial topological structures. By visualizing the spatial distribution of electric polarizations through angle-resolved piezoresponse force microscopy, we provide direct evidence for the spontaneous emergence of nontrivial topological polar structures. These results provide useful insights into the domain behavior of layered ferroelectric thin films.