Traditional urban and transport infrastructure planning that emphasized motorized transport has fractured public space systems and worsened environmental quality, leading to a decrease in active travel. A novel multiscale simulation method for supporting an integrated transportation infrastructure and public space design is presented in this paper. This method couples a mesoscale agent-based traffic prediction model, traffic-related emission calculation, microclimate simulations, and human thermal comfort assessment. In addition, the effects of five urban design strategies on traffic pollution and pedestrian level microclimate are evaluated (i.e., a “two-fold” evaluation). A case study in Beijing, China, is presented utilizing the proposed urban modeling-design framework to support the assessment of a series of transport infrastructure and public space scenarios, including the Baseline scenario, a System-Internal Integration scenario, and two External Integration scenarios. The results indicate that the most effective way of achieving an environmentally- and pedestrian- friendly urban design is to concentrate on both the integration within the transport infrastructure and public space system and the mitigation of the system externalities (e.g., air pollution and heat exhaustion). It also demonstrates that the integrated blue-green approach is a promising way of improving local air quality, micro-climatic conditions, and human comfort.