Manipulating materials of different dimensions into heterogeneous nanofiltration membranes with unique physicochemical properties and molecular sieving channels provides an effective way for accurate and fast molecular separation. Here we introduce a heterogeneous structure hybrid connection strategy to fabricate biodegradable wood-based covalent organic framework (COF) composite membranes. As a proof of concept, 3D Picea jezoensis (Siebold & Zucc.) Carrière was selected as the substrate of the membrane and in situ growth of 2D iCOF selective layers. Effective modulation of iCOF layers by 1D sulfonated polyaryletherketone (SPEEK-Na) using the “needle and thread” method. The rearrangement of the above multidimensional materials formed charge-regulated properties of laminar nano-channels and smooth hydrophilic contact area, thereby endowing specific molecular transport pathways and sieving capability for efficient dye/salt separation under ultra-low pressure of 0.5 bar. The wood-based heterostructured membranes exhibited high dye rejection (>97 %), low salt rejection (<10 %), and high permeance (172.34 L m−2 h−1 bar−1), which is superior to many reported dye/salt separation membrane materials. In addition, the system exhibited a certain degree of operational stability, good antifouling, and soil biodegradability. Overall, this work enables the design and fabrication of heterostructured separation membranes to be obtained from nature and used in nature, resulting in efficient and sustainable water purification applications.