Graphene oxide membrane (GOM) possesses ultrafast and tunable two-dimensional water transport pathways, making it an ideal candidate for nanofiltration separation of dye wastewater. However, GOM also faces great challenges such as poor aqueous stability, collapse of non-oxygenated regions under high pressure, and limitations imposed by trade-off effects. In this study, covalent organic frameworks (COFs) were in-situ formed within GOM interlayers and on membrane surface to enlarge interlayer spacings and enhance hydrophilicity of GOM simultaneously via a two-step method including monomer retention in GOM and in-situ confined interfacial polymerization of COFs. Fourier transformation infrared spectroscopy (FT-IR) and X-ray photoelectron spectrometry (XPS) results confirmed the successful synthesis of COF on GOM surface, which enhanced membrane surface hydrophilicity and bridged the split defects of GOM. According to X-ray diffraction measurements (XRD) and scanning electron microscope (SEM) results, COF@GO membranes possessed enlarged interlayer spacings and increased thickness of selective layer, which indicated the successful intercalation of COF into GO interlayer. COF@GO-50 membrane exhibited an ultrahigh pure water permeability (PWP) of 148.1 L/(m2·h·bar), with 99.0 % rejection for direct red 80 (DR80) aqueous solution and 9.6 % NaCl rejection. The ultrahigh water permeance might be ascribed to the enlarged interlayer pathways, the shortened vertical pathways provided by in-plane pores of COF nanosheets, and enhanced water adsorption capacity due to enhanced membrane hydrophilicity. Moreover, COF@GO nanofiltration membrane demonstrated excellent anti-fouling properties and long-term stability in 30h continuous operation, maintaining considerable separation efficiency under harsh conditions. This work provides a straightforward and applicable strategy to simultaneously enlarge interlayer spacings and enhance surface hydrophilicity of GOM via in-situ confined preparation of COFs, achieving ultrahigh water permeance and overcoming the trade-off effect between permeability and selectivity of GOM.