Faced with the complexity of the social environment and the heterogeneity of people’s public welfare needs，cross-border cooperation in public welfare has become a common choice among the three major departments of public welfare，government，and enterprise. Cross-border cooperation in public welfare is a dissipative structural system with characteristics of openness，non-equilibrium，nonlinear interactions，and fluctuations. This dissipative structural feature will generally promote the system to evolve from disorder to order. From the perspective of dissipative structure theory，it is found that the current cross-border cooperation system for public welfare in China has problems such as limited openness，homogeneous output，poor cooperation operation，and negative interference from fluctuations. In response to the above issues，it is necessary to broaden cooperation space to enhance system openness，innovate services to drive the system away from equilibrium，strengthen integration to play a non-linear role among the subjects，and explore and utilize key factors to cultivate effective fluctuations in the public welfare cross-border cooperation system based on an overall understanding of the dissipative structure mechanism. This promotes the updating and evolution of the cross-border cooperation system for public welfare，and enhances the supply side capacity of public welfare and charity.