In this work, we exploited the notable advantages of using three‐dimensional covalent organic frameworks (3D COFs) as supports for efficiently and controllably loading Pd. Tetraphenylmethane based 3D COF (TPM‐3D‐COF‐BPY) bearing bipyridine as coordination sites was constructed. A 7‐fold interpenetrated dia structure was revealed by the aid of powder X‐ray diffraction (PXRD) and structural simulation. The unique side‐by‐side 1D channels of TPM‐3D‐COF‐BPY provide enormous easily accessible active surface areas for heterogeneous catalysis throughout the topological structure. The delicate 7‐fold interpenetration of the bipyridine linked frameworks yields discrete and widespread coordination sites and enables super‐efficient heterogeneous catalysis after metalation of nitrogen coordination sites in TPM‐3D‐COF‐BPY. As a demonstration, Pd(II) was selectively anchored to the bipyridine coordination sites in the TPM‐3D‐COF‐BPY matrix. Further reduction of Pd(II) loaded in the topological structure leads to highly dispersed ultrafine Pd nanoparticles (NPs) with an average size of 1.12 nm confined within channels of TPM‐3D‐COF‐BPY. The as‐prepared Pd@TPM‐3D‐COF‐BPY as heterogeneous catalyst exhibits excellent efficiency, stability, and recyclability in catalyzing the Suziki‐Miyaura coupling reactions reaching a 98% yield within 2 h under facile conditions.