Abstract: The Low-altitude Economy is an important component of the New Quality Productive Forces, and the sound and sustainable development of the Low-altitude Economy is based on strict safety guarantees. Emerging safety risks derived from Low-altitude Economy activities include aviation safety risks, public safety risks, national information security risks and personal privacy security risks, and are characterized by the plurality of generating and bearing subjects, the arbitrariness of generating time and space, and the asymmetry of risk realization costs and governance costs. As far as the relationship between safety risks and the development of the Low-altitude Economy is concerned, the complete logical chain of risk evolution suggests an interaction with the development of the Low-altitude Economy itself. First, the development of economic efficiency leads to airspace reform. Secondly, airspace reform leads to changes in the powers (rights) structure. Thirdly, the diversification of powers (rights) leads to the evolution of safety risks. Finally, the emerging safety risks hinder the development of the Low-altitude Economy. However, China’s existing legal system, governance mechanisms, and governance tools cannot effectively regulate and prevent new safety risks caused by the Low-altitude Economy. With regard to the legal system, the existing legal system lags behind practice at the macro level, and some of the rules are characterized by rigidity. In addition, some of the new legal documents are fragmented and even contradictory. In terms of governance mechanisms, there are problems such as chaotic governance institutions, unclear responsibilities and a single structure of governance bodies. In terms of governance tools, there are still problems such as difficulties in law enforcement and high enforcement costs. The concept of Agile Governance aims to change the way policy operates in the fourth industrial revolution, and it is characterized by more progressive features. First, it is responsive. Agile Governance is more time-sensitive than the traditional plan-based policy-making approach. On the one hand, Agile Governance places more emphasis on rapid response to the object of governance and real-time optimization of governance behaviors, thus achieving the dual efficacy of immediate handling and risk prevention. On the other hand, Agile Governance can also realize the continuous iteration of governance policy and governance itself. Secondly, the multi-stakeholders of governance. Agile Governance advocates the adoption of a new paradigm that goes beyond government governance and allows more stakeholders to participate in governance. As a policymaker, the government should share the “workload” of constructing, monitoring and optimizing the governance system or policy with private entities and citizens’ groups in order to realize the checks and balances among different stakeholders and to make the process of policy-making and the policies formulated more inclusive and human-centered. Agile Governance’s characteristics of rapid response, multi-stakeholders, and continuous iteration reveal its natural interrelationship with emerging safety risks. In order to promote the high-quality and sustainable development of the Low-altitude Economy on the basis of effective prevention of emerging safety risks, firstly, the construction of “hard law” and “soft law” should be coordinated to help construct a governance legal system that balances economic development and safety protection; secondly, the powers and functions of the main public governance authorities should be clarified and synergy should be strengthened, and the effectiveness of the autonomy of other multi-stakeholders should be emphasized; and thirdly, it is necessary to innovate governance tools by improving infrastructure and promoting the integration of technological tools in order to achieve mutual good governance of emerging safety risks.