Abstract: Conventional three-dimensional woven composites (3DWCs) usually employ a single periodic architecture, which makes it difficult to meet different requirements for load-carrying capacity and damage tolerance within one component. To enable region-specific mechanical design, this study proposes a multi-structure 3D woven composite in which different woven architectures are continuously arranged along the warp direction. A shallow-crossing layer-to-layer angle-interlock architecture (structure A), a twill-like layer-to-layer angle-interlock architecture (structure B), and a satin-like layer-to-layer angle-interlock architecture (structure C) were selected as the basic structural units. Warp-direction three-point bending tests were conducted on different structural configurations. A parametric modeling method and a subcell-based multiscale finite element model were also developed to investigate their flexural response and damage behavior. The results show that the architecture at the midspan mainly controls the initial flexural stiffness and overall response, while the spatial arrangement of different architectures has a stronger effect than their relative proportions. For the A/B combinations, placing the stiffer structure B at the midspan increases the overall load-carrying capacity, but also increases the curvature discontinuity near the A/B transition and promotes premature transverse damage in the weft yarns. For the B/C combinations, increasing the proportion of structure B from 51.0% to 80.4% increases the peak flexural strength by about 8.2%, while the curvature difference across the transition increases from 0.0007 mm⁻¹ to 0.0021 mm⁻¹ and the damage becomes more localized. When structure C is introduced between structures A and B, the curvature difference of approximately 0.0024 mm⁻¹ at the direct A/B transition is redistributed into two smaller differences of approximately 0.0009 mm⁻¹ and 0.0014 mm⁻¹ at the A/C and C/B interfaces, respectively. This indicates that structure C has the potential to improve deformation compatibility between structures A and B. A segmented-beam model can also provide a rapid estimate of the apparent flexural modulus for most symmetric multi-structure configurations. These results clarify the coupled effects of structural arrangement, stiffness gradient, and transition location on the flexural deformation and failure of multi-structure 3DWCs, and provide a basis for region-specific structural design.