Deeply integrated vulnerability and its evaluation framework provide a new perspective for the study of socio-ecological systems in metropolitan suburbs. A new vulnerability evaluation system of ‘exposure-sensitivity-adaptability’ based on the socio-ecological system and vulnerability theory was constructed. Meanwhile, drawing on the concept of ‘spatial trap’, the concept of ‘spatial vulnerability trap’ was tried to put forward. The spatial-temporal interaction characteristics were analyzed, the existence of spatial vulnerability trap was tested and the interaction mechanism of vulnerability dynamic evolution was revealed using spatial-temporal exploration analysis method and geographic detector for socio-ecological system vulnerability of 184 administrative villages in Qingpu District from the year 1998 to 2018. The results showed that: (1) During the study period, the socio-ecological systems vulnerability of Qingpu District increased from 0.518 to 0.621, and the vulnerability level increased from low grade to medium grade. The spatial-temporal pattern showed the dynamic characteristics of first increase and then decrease and high in the East and low in the west. (2) The relative length of the socio-ecological systems vulnerability temporal path movement in Qingpu District from 1998 to 2018 showed a trend of gradual decline from the central region to the surrounding area. The mobility curvature of the vulnerability time path was relatively small, showing the spatial pattern of low in the north and high in south, and the cohesion index of the spatial transition of vulnerability is 0.496. The spatial agglomeration structure had relatively high transfer activity and low path locking. (3) No ‘spatial vulnerability absolute trap’ was detected during the study period, yet the ‘spatial vulnerability relative trap’ highlighted in the 11 administrative villages mainly distributed around the administrative boundary in the north and south of the area. (4) Social capital factor, human capital factor, social factor, economic factor, ecological factor and financial capital factor are the main factors influencing the vulnerability change, but the influence of each factor showed fluctuation and type difference. The main interaction types of socio-ecological system vulnerability differentiation in urban suburbs are the cumulative type of internal and external coupling, the type of endogenous capacity constraint and the external environmental stress type. The results of the study are of great theoretical and practical significance to guide the suburban areas to prevent the vulnerability risk, promote regional coordination to reduce vulnerability and sustainable development.