MFI type zeolites with 10 membered-ring pores (~0.55 nm) have the ability to separate p-xylene from its bulkier isomers. Despite progress in developing p-xylene selective MFI membranes, the relationship between membrane micro-structures and separation performances remains elusive. Here, we introduced non-zeolitic micropores (ca. 0.6-1.5 nm) and mesopores (ca. 2-7 nm) to a conventional microporous MFI type zeolite membrane, yielding an unprecedented Swiss cheese-like hierarchical membrane structure. Specifically, the self-pillaring twinned MFI growth around MEL cores during secondary growth was key for creating these additional, non-zeolitic pores. The uniform, embedded non-zeolitic pores allowed for reducing defect formation considerably and facilitating molecular transport, resulting in high p-xylene perm-selectivity and molar flux. Specifically, compared to a conventional, crack network-containing MFI membranes of similar thickness (~1 µm), the mesoporous MFI membranes showed almost double p-xylene permeance (~1.6 ± 0.4 × 10-7 mol·m-2·s-1·Pa-1) and a high p-/o-xylene separation factor (~53.8 ± 7.3 vs. 3.5 ± 0.5 in the conventional MFI membrane) at 225 °C. Crucially, the embedded non-zeolitic pores allowed for decreasing the separation performance degradation, which was apparently related to coke formation; this was conceptually analogous to the decreased deactivation via the introduction of mesopores to microporous catalysts.