Mixed matrix membranes (MMMs) hold great promise in overcoming the tradeoff between membrane permeability and selectivity. The rational design of fillers to well coordinate physical and chemical selectivities remains challenging. Here, we explore a heterostructured filler by in-situ growth of ZIF-8 on LDH surface (ZIF-8@LDH), which was then embedded into Pebax to fabricate MMMs for CO2/CH4 separation. The proximity effect of the heterostructured filler endows MMMs with superior gas separation performance compared with the control MMMs containing single filler ZIF-8, LDH and dual fillers (where ZIF-8 and LDH are separately incorporated). On one hand, ZIF-8 and abundant hydroxyl groups on LDH afford favorable affinity toward CO2, significantly enhancing the physical selectivity of CO2/CH4. On the other hand, the oriented distribution of ZIF-8 on LDH elevates CO2 concentration around LDH and increases the efficiency of CO2 facilitated transport, leading to remarkably enhanced chemical selectivity. Particularly, the optimum separation performance is achieved for MMMs containing 2 wt% of ZIF-8@LDH with a CO2 permeability of 1307 Barrer and a CO2/CH4 selectivity of 31.6. The unique attributes of heterostructured filler may be extended to fabricate a variety of MMMs for high performance molecular separations.