The fragmentation of ecological network structures has become a common problem faced by cities. By establishing the urban ecological network under a specific socio-ecological system framework, we aimed to propose a quantitative index to diagnose the fragmentation of the network structure, and to construct detection model to explore the driving factors and mechanism of the network fragmentation. Using Shenzhen City as an example, we used the Floyd-Prim algorithm to generate the skeleton structure of the ecological network and construct a density discontinuity index to diagnose network fragmentation. Combined with the ecological network scenario, social-ecological system framework and a two-layer indicator system were constructed. The detection models were then established to explore the drivers of network disruption and their mode of impact. The models show that the average degree of network fragmentation in Shenzhen was 0.13, and the density of about 85% of corridor discontinuities was greater than 0.01, reflecting the serious state of structural fragmentation. Corridors with more severe structural fragmentation have poorer social-ecological coordination. The fragmentation in Shenzhen was mainly affected by the activities of actors (A) at the microlevel and the resource system (RS) at the macrolevel. The methods and the framework of socio-ecosystem analysis proposed in this paper can reveal the driving factors and influence modes of network fragmentation, providing decision-making reference for ecological restoration practice in urbanized areas.