Abstract: "Top-level design" plays a crucial role in the modernization of China's system and capacity for governance in the new era. It is not merely a technical concept in the administrative sense, but an important governance philosophy that profoundly embodies the core logic of Marx and Engels' state theory. The class nature, historical nature, and relative autonomy of the state constitute the core logic of Marx and Engels' state theory, particularly their views on the state's relative autonomy. The governance philosophy of "top-level design" in the new era represents, to a large extent, an adherence to and innovation upon this core logic, and on that basis, has introduced innovative approaches to specific aspects of state governance. First, through consulting the people and serving the people, it achieves the integration of the state's relative autonomy with the people-centered approach, realizing the contemporary development of Marx and Engels' view that the relative autonomous characteristics of the state possess class nature. Second, through adhering to the coordination between top-level design and "crossing the river by feeling the stones", it flexibly adjusts policies and strategic deployments to adapt to the developmental needs of different historical stages, fully demonstrating Marx and Engels' assertion that the relative autonomous characteristics of the state possess historical nature, and on that basis, it has introduced innovative practices in the substance of governance. Finally, through emphasizing the maintenance of the CPC Central Committee's authority and centralized, unified leadership, focusing on state capacity building, and emphasizing the methodological strategy of overall planning, it interprets the effective application and enriched development of the core characteristic of "relative autonomy" in Marx and Engels' views on the state's relative autonomy in contemporary times, and on that basis, has introduced innovative practices in the substance of governance. It can be seen that the governance philosophy of "top-level design" in the new era represents an adherence to and innovation upon Marx and Engels' state theory, providing powerful momentum for advancing the modernization of China's system and capacity for governance and even the entire Chinese path to modernization.