In the digital era, “flow cities” face a governance paradox where flow development is accompanied by inherent risks. Driven by technological optimism, urban competition orientation, and the methodological limitations in addressing flow risks, existing studies exhibit an obvious “positive bias” that is, they mostly focus on the developmental effects of “flow cities” while neglecting the associated risks underlying the development orientation. To address the gaps in existing research, this study, based on the social amplification of risk framework (SARF), constructs an analytical framework from three dimensions—endogeneity, spatiality, and sociality—to reveal the formation process of risks in “flow cities”. This paper argues that risks in “flow cities” follow an amplification path of “endogenous alienation–spatial superposition–social polarization”, which is driven by the joint action of multiple factors. Specifically, technology activates the risk genes of “flow cities”, inducing endogenous alienation; the coupled diffusion of multiple flows (such as human flow, material flow, and information flow) leads to spatial superposition; and the algorithm-society nesting results in governance lag, exacerbating social polarization. Compared with traditional urban risks, risks in “flow cities” exhibit significant differences in dimensions such as risk types, diffusion characteristics, spatial attributes, and amplification mechanisms, and thus differ in governance focus, logic, and objectives. Accordingly, this study proposes constructing a risk governance chain centered on flows, which consists of the external circulation path for flow development and the internal circulation path for risk governance. This chain forms a full-process, full-cycle risk governance system, including high-quality flow aggregation based on risk early warning, high-level flow utilization based on risk regulation, high-standard flow restriction based on risk assessment, and high-value flow guidance based on risk resolution, providing both theoretical support and specific measures for balancing urban flow development and risk governance.