Carbon nanomaterials have huge application prospects in the fields of materials science and biomedicine. Graphene oxide (GO) can be served as an excellent carrier with good loading capacity and biocompatibility. However, lamelayers of GO are prone to aggregation and difficult to stably disperse in solution. Only relying on the mesh graphene sheets as a carrier still cannot achieve a good loading efficiency. Therefore, oriented layered graphene oxide pad (OGO) is synthesized and used as a carrier for ligand fishing. The structure of OGO exhibits good reproducibility and recyclability, and its regular open channels and low pore curvature can effectively ensure a high density of fishing sites and flow speed, improving the loading capacity and storage stability. According to the amount of immobilized cell membranes protein (CMP), OGO can reach 1.5 to 2 times loading capacity of GO. The established CMP@OGO is stable within 48 h at 4 °C, and the reuse rate of OGO is 93.04 ± 0.67%. Finally, salvianolic acid B, deoxyshikonin, and shikonin were identified as potentially active compounds in comfrey combined with a high-performance liquid chromatography-hybrid linear ion trap/orbitrap mass spectrometer. It can provide a promising platform for OGO to screen active compounds in high throughput.