Topological indices are a class of numerical invariants that predict certain physical and chemical properties of molecules. Recently, two novel topological indices, named as Sombor index and reduced Sombor index, were introduced by Gutman, defined as $$SO(G)=\sum_{uv\in E(G)}\sqrt{d_{G}^{2}(u)+d_{G}^{2}(v)},$$ $$SO_{red}(G)=\sum_{uv\in E(G)}\sqrt{(d_{G}(u)-1)^{2}+(d_{G}(v)-1)^{2}},$$ where $d_{G}(u)$ denotes the degree of vertex $u$ in $G$. In this paper, our aim is to order the chemical trees, chemical unicyclic graphs, chemical bicyclic graphs and chemical tricyclic graphs with respect to Sombor index and reduced Sombor index. We determine the first fourteen minimum chemical trees, the first four minimum chemical unicyclic graphs, the first three minimum chemical bicyclic graphs, the first seven minimum chemical tricyclic graphs. At last, we consider the applications of reduced Sombor index to octane isomers.