Assessment and mapping of coastal habitat quality are critical for integrated coastal zone management. However, in the coastal zone, characterized as a terrestrial-marine continuum, few studies have incorporated land-sea connections while mapping and predicting the quality of habitats. In this study, we propose a novel framework that integrates an ecosystem service assessment model and global ecosystem classification, and within this framework, the cross-system threats from both ocean- and land-based human activities were considered. On this basis, by linking the threat sources of habitat quality with management policy scenarios, the prediction of habitat quality across land and sea was realized. Xiamen Bay, a typical intensively developed bay in Southeast China, was used as a case study. Thirteen habitat types and 12 threats were identified in the upland/supratidal, intertidal, and subtidal zones of Xiamen Bay. Each threat affected habitats in at least two coastal zone subdivisions. The results showed that by 2030, 26.9% of the total habitat area is expected to decline in quality, while 16.9% will improve. Intertidal habitats are especially vulnerable to multiple threats. Our study revealed a strong negative correlation between threat intensity and habitat quality changes. Eight of the 12 threats will be changed by the five coastal management policies, and six types of habitats are potential beneficiaries. Overall, local coastal zone management strategies will contribute to enhance the quality of intertidal and subtidal habitats, whereas upland/supratidal zone are anticipated to experience a decline. The tourism development policy may have negative impacts on all 13 habitats and cover the largest area, while the aquaculture regulation policy is expected to yield the greatest benefits. We revealed that cross-system threats are prevalent in coastal zone habitats, making it possible for coastal zone management policies to have cross-system impacts. The tool developed herein can support integrated coastal zone management in the terrestrial-marine continuum and facilitate effective decision-making.