A sustainable development system involves resource limitation, environmental stress and policy regulation, and the flow and integration of resources and factors on a multi-level spatial scale. However, it is difficult to meet the actual needs of local development through traditional single-scale and macro-scale evaluation of the comprehensive level. Taking Suzhou City as an example, based on the United Nations (UN) sustainable development goals (SDGs) framework, the entropy method and fuzzy comprehensive evaluation (FCE) were used to construct an evaluation index system of the municipal sustainable development level. Growth and obstacles of the sustainable development system and its subsystems were systematically analyzed on a multi-level spatial scale. Results show that during the study period (2000-2016), the sustainable development system in Suzhou was relatively low at the beginning of the study. With the passage of time, it generally developed in a stable, continuous, and balanced direction. The levels of development, deficiencies, and obstacle factors of sustainable development systems and their subsystems are significantly different between levels; especially during the study period, the order change between towns is significantly higher than the order change between districts. Within an evaluation unit, there is a process of rising and continuing growth among certain subsystems, but some subsystems have been developing slowly due to resource constraints, environmental load, etc., or their contribution to the level of sustainable development has remained low. The city sustainable development evaluation index system based on the SDGs framework can meet the requirements of regional assessment and has the potential for further promotion and use. The evaluation results can provide a necessary reference for the subsystem coordination, scale linkage, and resource space allocation of the sustainable development system in Suzhou.