As a critical element in urban sustainability efforts, green roofs (GRs) can reduce building energy use and enhance ecological performance via additional growing medium and plant layers. However, the extra building components result in increased load and structural thickness as well as construction complexity. This paper proposes a design-fabrication method for a thin-vaulted green roof prototype with a compressive-only surface and upstand ribs along unevenly distributed stress lines for a lightweight and material-efficient structure. The structural efficiency of the proposed roof has been proven high compared to conventional flat roof through simulation. To realize such a non-standard and multifunctional structure, a hybrid formwork system is presented to deal with geometric complexity and functional integration by treating stay-in-place formwork as a function part. In particular, 3D clay printing (3DCP) is selected as eco-friendly formwork staying in the GRs to integrate with plant growth substrate, leading to a more simplified and sustainable fabrication. An empirical construction experiment is conducted to validate the proposed method on a 1:5 scale.