Against the background of new urbanization, following the concept of "intensive, energy-saving, and ecological development," the idea of interactive development of transportation and land use, minimum energy consumption, and environmental damage is put forward. Regional comprehensive transportation network will become the main trend of low-carbon ecological comprehensive transportation planning strategy. Based on the three-level programming model, this paper studies the dynamic relationship between three planning levels and carries out comprehensive optimization design. Decision variables include characteristics of land use optimization, and also the construction and renovation of traffic routes. In order to solve the complex nonlinear model, the hybrid method of augmented dual algorithm and sequential average algorithm is adopted to solve the lower model, and the heuristic algorithm is adopted to effectively solve the integrated model, thus obtaining the optimal comprehensive transportation network layout scheme and the optimal land use scheme. Finally, a multi-scale space is taken as a research unit to carry out an example analysis. The results verify the effectiveness of the proposed model and method, which can improve the scientificity and rationality of the planning.