This research addresses the eco-system optimal dynamic traffic assignment (ESODTA) problem which aims to find system optimal eco-routing or green routing flows that minimize total vehicular emission in a congested network. We propose a generic agent-based ESODTA model and a simplified queueing model (SQM) that is able to clearly distinguish vehicles’ speed in free-flow and congested conditions for multi-scale emission analysis, and facilitates analyzing the relationship between link emission and delay. Based on the SQM, an expanded space-time network is constructed to formulate the ESODTA with constant bottleneck discharge capacities. The resulting integer linear model of the ESODTA is solved by a Lagrangian relaxation-based algorithm. For the simulation-based ESODTA, we present the column-generation-based heuristic, which requires link and path marginal emissions in the embedded time-dependent least-cost path algorithm and the gradient-projection-based descent direction method. We derive a formula of marginal emission which encompasses the marginal travel time as a special case, and develop an algorithm for evaluating path marginal emissions in a congested network. Numerical experiments are conducted to demonstrate that the proposed algorithm is able to effectively obtain coordinated route flows that minimize the system-wide vehicular emission for large-scale networks.