Featured with zero-carbon, jam-free, and high-capacity, the utilization of metro systems for collaborative passenger-and-freight transport (i.e., the metro-based underground logistics system, M-ULS) has been recognized as a favorable alternative to realize automated goods movement in future megacities. This paper proposes an equilibrium chance-constrained programming (ECP) approach for the M-ULS network planning problem (MULNP) considering uncertain demand and costs. Based on the ongoing satellite city development project, the layout formation, facility components, and transportation workflows of a two-tier M-ULS network are designed. The joint decisions (i.e., location, allocation, capacity, inventory, spoke pipeline layout, and flow routing) are formulated as an ECP model with conjoint objectives of minimal fixed cost, operating cost, and penalty cost due to low operating load, wherein the chance-based constraints are further reformulated into crisp equivalent form. To yield high-quality solutions for MULNP problem, an improved multi-objective cooperative co-evolutionary algorithm (MoCC) incorporating non-dominated sorting and chromosomal recombination strategy is proposed and then validated via two groups of instances. Results from the Beijing case study suggest that the proposed method has computational advantages over MoPSO and NSGA-II in acquiring Pareto fronts of large-scale MULNP. The best configurations and layout schemes of the M-ULS networks in both uncertain and deterministic scenarios are analyzed. Based on the findings, several insights for real-world M-ULS network decision-making are provided.