Transit-oriented development (TOD) has a close relationship with ecology since its inception and aims to create livable and sustainable environments. However, few studies have examined the key point of ecology in the construction of TOD assessment models. This paper takes Odawara as an example, a city located on the outskirts of the Tokyo metropolitan area. Based on the node–place model, a new dimension of ecology is introduced to expand the two-dimensional model into a three-dimensional model, primarily applied to 18 stations in Odawara. Using this model, the study explores the impact of TOD on the development process of Odawara and proposes historical policy and data-based current condition discussions. The results indicate that the model-based analysis reveals a discrepancy between the current condition of the 18 stations in Odawara and the official positioning of these stations by city managers. Additionally, there is a negative correlation between the node–place value and ecology value of the station areas. We believe that this approach not only directly connects TOD with ecological considerations but also develops a new quantitative assessment model for TOD, particularly in the context of abundant ecological resources in suburban areas of metropolitan areas, arriving at a more refined level of research than before. At the same time, the model continues to maintain good scalability, providing new perspectives for the metabolism of developing areas worldwide.