The development of high-performance mixed matrix membranes (MMMs) with satisfactory structure stability has attracted much attention for the past few years. The rational design and synthesis of fillers to well coordinate themselves in the polymeric matrix is still challenging. The core-shell structured fillers were synthesized via the heteroepitaxial growth of ZIF-8 on ZIF-L(Co) surface (ZIF-L(Co)@ZIF-8), which were then embedded into Pebax to fabricate MMMs for enhanced CO2/CH4 separation. The synthesized fillers and MMMs were characterized via SEM with EDS mapping, TEM, XRD, FIIR and nanoindentation measurements. The effects of ZIF-L(Co)@ZIF-8 loading and filler components on gas separation performance were studied with the evaluation of membrane stability. The experimental results indicated that the filled ZIF-L(Co)@ZIF-8 could be evenly distributed within the bulky Pebax. The synergistic effect of the core-shell structured fillers in adsorption and molecular sieving endowed the synthesized MMMs with superior gas separation performances. The optimal separation performance is achieved for the MMM containing 3 wt% of ZIF-L(Co)@ZIF-8 with a CO2 permeability of 145.7 Barrer and a CO2/CH4 selectivity of 40.9, corresponding to 79.1% and 110.1% increases over pure Pebax membrane.