For a lattice polytope $P$, the rank of $P$ is defined by $F-(\dim P+1)$, where $F$ is the number of facets of $P$. In this paper, we study matroid polytopes with small rank. More precisely, we characterize matroid independence polytopes and graphic matroid base polytopes with rank at most three. Furthermore, using this characterization, we investigate their relationships with order polytopes, stable set polytopes, and edge polytopes.