Two-dimensional (2D) covalent organic frameworks (COFs) fabricated through on-surface synthesis were investigated as a honeycomb nanopore template for the growth of 3d-transition-metal nanoclusters (NCs) with a size of 2 nm on a metallic substrate. The evolution of these NCs and their electronic characteristics were studied employing scanning tunneling microscopy/spectroscopy (STM/STS), angle-resolved ultraviolet photoelectron spectroscopy (ARUPS), and X-ray photoelectron spectroscopy (XPS) under an ultrahigh-vacuum (UHV) condition at room temperature. The 2D COFs were synthesized on Cu(111) substrate utilizing 1,3,5-tris(4-bromophenyl)benzene (TBB) precursors, which engendered a honeycomb nanopore array of approximately 2 nm in size. In contrast to the behavior observed in the Co/Cu( 111) system producing triangular-shaped bilayerstacking nanoclusters measuring 10−20 nm, STM imaging of Co/COFs/Cu(111) revealed the growth of Co NCs of approximately 1.5 nm within a single COF nanopore. This growth occurred without forming a monolayer film beneath the COFs, providing direct evidence that the 2D COFs on Cu(111) can effectively entrap Co atoms within the nanopore, giving rise to Co NCs. Spectroscopy measurements, including STS/UPS/XPS, confirmed the different local densities of states for Co NCs and COFs, corroborating the coexistence of Co NCs and COFs on the surface.