Flexible grade control structures (GCSs) are increasingly popular alternative countermeasures consisting of conventional solid structures for protecting riverbeds from erosion. Among this structure typology, tetrahedron framed permeable weirs (TFPW) were proposed to stabilize riverbeds and protect cross-river structures. The bed morphology as well as the interactions among the structures, water flow and bed features have not been systematically analyzed. Therefore, based on the field data collected in the Jianjiang River, a series of physical model experiments were carried out in this study to investigate the river morphology in unstable gravel-bed rivers under five different structural conditions, including no GCSs, solid bed sills and flexible TFPW with three different layout types. Data on bedform features, topography changes and the volume of erosion or deposition were collected and analyzed. The results indicated that dramatic general erosion and bed armoring would occur without any protection. The bed would be protected from upstream erosion with bed sills, but, at the same time, in addition to general erosion and bed armoring downstream of the structures, deep local scour might pose a serious threat to structural safety. TFPW had good protective effects on riverbeds by preventing the bed from erosion and even inducing sediment deposition both upstream and downstream from the structures. Because the flexible structures have advantages in ecology, structural stability and construction, TFPW were suitable and optimal for riverbed stabilization in unstable gravel-bed rivers.