In this paper we compare the $\mathbb J$-stratification (or the semi-module stratification) and the Ekedahl-Oort stratification of affine Deligne-Lusztig varieties in the superbasic case. In particular, we classify the cases where the $\mathbb J$-stratification gives a refinement of the Ekedahl-Oort stratification, which include many interesting cases such that the affine Deligne-Lusztig variety admits a simple geometric structure.