The 14th five-year plan proposes to formulate an action plan for peaking carbon emissions by 2030 and anchor efforts to achieve carbon neutrality by 2060. High-quality carbon emissions have become one of the important objectives of China’s high-quality economic development in the future. City is the main spatial carrier of China’s development, so high-quality carbon emission should be realized under the “two horizontal and three vertical” urbanization pattern with urban agglomeration as the core. In this regard, carbon neutrality is embedded into the system dynamics (SD) model as the main control factor, and a high-quality development SD model of China’s urban agglomeration under the “dual carbon” goals is constructed. The data and system parameters in 2019 are used to simulate and predict the carbon peak and carbon neutrality of urban agglomeration in 2030 and 2060 under different development scenarios. The results show that: ① the authenticity test shows that the simulation effect of the model is good and operable. ② Under the benchmark scenario, the “dual carbon” goals are difficult to achieve, and the carbon emission system is on the verge of collapse. However, under the high-quality development scenario, except for the central urban agglomeration, other urban agglomerations can achieve the “dual carbon” goals within the time limit proposed in the 14th five-year plan. ③ In order to achieve the “dual carbon” goals in the process of high-quality development of urban agglomeration, it is necessary to clarify that low-carbon technology is an important means, industrial transformation is the key, and to realize the systematic reform of energy and industrial structure.