Mode shifting is an effective solution to improve transport sustainability. This study developed an indicator system for measuring mode-based transport sustainability at the local level, and the results provided a basis for evaluating the proposed improvement solutions. A case study of Taipei and Kaohsiung confirmed that the mode-based transport sustainability model could highlight which mode provided the most superior transport sustainability and which indicator or aspect could be improved to enhance the transport sustainability of the two cities. The findings from Taipei and Kaohsiung revealed that the use of Mass Rapid Transit (MRT) and bicycles significantly improved transport sustainability, but that the effects of motorcycle use on transport sustainability varied according to local circumstances. Analysis of four transport sustainability improvement scenarios indicated that building bicycle exclusive lanes would have significant environmental and social benefits both in Taipei and Kaohsiung. Increasing parking fees for cars and motorcycles would have a relatively insignificant effect on improving sustainability in Taipei City. Constructing an infrastructure for electric motorcycles in Kaohsiung would provide the most significant improvement to transport sustainability of any of the four scenarios.