Covalent organic frameworks (COFs) with precisely controllable structures and highly ordered porosity possess great potential as electrocatalysts for hydrogen evolution reaction (HER). However, the catalytic performance of pristine COFs is limited by the poor active sites and low electron transfer. Herein, to address these issues, the conductive carbon nanotubes (CNTs) are coated by a defined structure RuBpy(H2O)(OH)Cl2 in bipyridine‐based COF (TpBpy). And this composite with single site Ru incorporated can be used as HER electrocatalyst in alkaline conditions. A series of crucial issues are carefully discussed through experiments and density functional theory (DFT) calculations, such as the coordination structure of the atomically dispersion Ru ions, the catalytic mechanism of the embedded catalytic site, and the effect of COF and CNTs on the electrocatalytic properties. According to DFT calculations, the embedded single sites Ru act as catalytic sites for H2 generation. Benefitting from increasing the catalyst conductivity and the charge transfer, the as‐prepared c‐CNT‐0.68@TpBpy‐Ru shows an excellent HER overpotential of 112 mV at 10 mA cm−2 under alkaline conditions as well as an excellent durability up to 12 h, which is superior to that of most of the reported COFs electrocatalysts in alkaline solution.