In the era of digital intelligence, sustainable ecological cooperation in cross-border integration has become a trend, and the willingness of sustainable cooperation is the key to stabilising the cooperative relationship between enterprises and partners and obtaining more profits. Due to the heterogeneity of enterprises, the sense of fairness of enterprises in a relatively disadvantaged position can only be improved to achieve the sustainable development of the cooperative relationship between the two parties. In the business ecosystem, there are some enterprises with obvious differences in resource endowment, market influence, innovation engines, and technology leadership, etc. Enterprises with core competitive advantages occupy the ecological high position and become the ecological core enterprises, while enterprises with relatively weak competitive advantages need to depend on the core enterprises in order to survive in the business ecosystem and become the ecological participating enterprises. This paper takes ‘core enterprise–participating enterprises’ as the main body, establishes a dynamic evolutionary game model to explore the factors affecting the two parties ‘willingness to sustain cooperation, and finds that the increase in the coefficient of willingness to sustain cooperation and the coefficient of maintaining the relationship between core enterprises and participating enterprises, as well as the decrease in the losses caused by opportunistic behaviours of the other party’s enterprises to their own enterprises, will promote the two parties’ willingness to sustain cooperation. In order to verify the connection between the numerical model derivation and the actual situation, we refer to the research of domestic and international scholars, design the scale, and finally obtain 242 valid questionnaires through the research of 263 small and medium-sized enterprises (SMEs) in China. The results find that the sense of distributive fairness, procedural fairness, and interactive fairness positively promote the willingness to cooperate on a sustainable basis; the sense of contractual fairness increases the willingness to cooperate on a sustainable basis through the relationship value enhancement; and the risk of opportunism negatively moderates the relationship value’s impact on the willingness to cooperate on a sustainable basis. The findings can provide lessons for Chinese SMEs to achieve cross-border integration and for SMEs to improve their ability to manage partnership uncertainty.