The exploitation of competent isolation and purification technology of methane (CH4) is an imperative and challenging task for full utilization of clean natural gas in petrochemical industry. Compared to traditional energy-intensive low-temperature distillation, adsorptive separation using porous metal–organic framework (MOF) materials provides an alternative technique with low energy consumption and high efficiency. In this situation, an aromatic pore engineering strategy in a series of pillar-layered Zn-based MOFs by introducing organic linkers with different degrees of aromatic units was investigated to tune pore size and pore environment for simultaneously removing propane (C3H8) and ethane (C2H6) from C3H8/C2H6/CH4 mixtures. Compared to the other two analogues, i.e. Zn(BDC)(TED)0.5 and Zn(ADC)(TED)0.5, obtained Zn(NDC)(TED)0.5 showed high adsorption capacity for C3H8 (5.18 mmol/g) and C2H6 (5.04 mmol/g) and selectivity for C3H8/CH4 and C2H6/CH4 at 298 K and 1.0 bar. Breakthrough tests proved the three MOFs can effectively separate ternary C3H8/C2H6/CH4 mixtures, and Zn(NDC)(TED)0.5 especially exhibited excellent high-purity CH4 yield of 10.07 mmol/g. Computational simulations showed that suitable pore space and surface aromatic environment in Zn(NDC)(TED)0.5 created beneficial interactions with C3H8 and C2H6 molecules, which ultimately contributed to its favourable adsorption and separation property. This system work provides insights for the development of pore control method in MOF materials for natural gas purification.