The regional sustainable development level, sustainability of regional development, and system coordination are the three components comprising regional sustainable development assessments. Traditional methods determining entire sustainable development system levels, including the sustainable development level of societies, economies, and environmental subsystems, using principal component analyses (PCA) are problematic. The sustainable development of the Bohai Rim region, including two municipalities and three provinces in China, is affected by extreme conflicts between socioeconomic development and environmental pollution. We proposed a model coupling nonlinear principal component analysis and Gram-Schmidt orthogonalization (NLPCA-GSO), and provided a holistic regional sustainable development assessment method, including the sustainable development level, sustainability of regional development, and system coordination, in a single society-economy-environment system, using the Bohai Rim region as a case study. The evaluation framework, including the NLPCA-GSO, sustainability of regional development (SRD), and sustainability coordination (SC) models, was initially constructed, and was composed of three modules as three steps in the specific analysis. In the first module, the three subsystems in the sustainable development level were emphasized by NLPCA when the variables were selected, and the comprehensive level of the entire sustainable development system was highlighted by GSO when the different base vectors were determined; in second module, we focused on the dynamic potential of regional development and showed sustainability through the acceleration of the entire sustainable development level between each sample compared to first sample; and in third module, the sustainability of all subsystems was compared and the system coordination changes were emphasized, with a filtering analysis of sustainable development system changes presented. The present study emphasized a novel approach to determine the sustainable development level of several subsystems and to overcome the incomparability of PCA results among subsystems. NLPCA was used to overcome traditional PCA deficiencies in complex and multidimensional sustainable-development systems, and the eigenvector direction was determined to avoid distorted results. The results showed that the NLPCA-GSO model evaluated all the subsystems comprehensively; and the SRD and SC models graphically demonstrated the essential and connotation of sustainable development; the empirical study indicates that the Bohai Rim region has experienced a distinct development period, and while sustainability remained low, the sustainable development level and sustainability coordination increased slightly during the study period, possibly caused by the decrease of the environmental subsystem sustainability. Obviously, resources, energy, and ecological environmental factors cannot be substituted by physical or human capital only as the essential inputs in economic production, consumption, or welfare. The present study enriches the sustainable development assessment theory and methodology, and lays the foundation for further sustainable development research in the Bohai Rim region.