The energy systems are evolving into heterogeneous energy systems (HESs) with complicated integration of sources, networks, loads, and storage towards a decarbonized future of human beings. This paper develops the flexible allocation and optimal configuration of multi-level energy exploitation units (MEEUs) for the HES considering resource distribution including local energy conditions and actual coupled relationship of various energy networks. A bi-level optimal planning model of MEEUs for the HES considering initial investment cost, carbon emission cost, operation cost and line loss is developed to figure out the optimal location, structure, configuration and corresponding operation strategy. To address the non-convex and non-linear model, a novel hybrid solution method considering the mixing characteristics of mixed-integer second-order cone programming (MISOCP) model and quadratic non-convex model is proposed. The solution method adopts MISOCP model for figuring out the optimal location, structure and configuration of MEEUs and quadratic non-convex model for optimal operation strategy of MEEUs, which not only improves the computational efficiency but also ensures the solution accuracy. Finally, the related case studies are conducted to compare the proposed MEEU and distributed energy storage unit (DESU) in terms of energy consumption, renewable energy absorbency, carbon emission and line loss. The results verify the significant improvement of the comprehensive energy efficiency, the investment potentiality and the environmental benefits obtained by the proposed planning model.