This study investigates a multimodal green logistics network design problem of urban agglomeration with stochastic demand, in which different logistics authorities among the different cities jointly optimize the logistics node configurations and uniform carbon taxes over logistics transport modes to maximize the total social welfare of urban agglomeration and consider logistics users’ choice behaviors. The users’ choice behaviors are captured by a logit-based stochastic equilibrium model. To describe the game behaviors of logistics authorities in urban agglomeration, the problem is formulated as two nonlinear bilevel programming models, namely, independent and centralized decision models. Next, a quantum-behaved particle swarm optimization (QPSO) embedded with a Method of Successive Averages (MSA) is presented to solve the proposed models. Simulation results show that to achieve the overall optimization layout of the green logistics network in urban agglomeration the logistics authorities should adopt centralized decisions, construct a multimode logistics network, and make a reasonable carbon tax.