As an efficient molecular engineering approach, on-surface synthesis (OSS) defines a special opportunity to investigate intermolecular coupling at the sub-molecular level and has delivered many appealing polymers. So far, all OSS is based on the lateral covalent bonding of molecular precursors within a single molecular layer; extending OSS from two to three dimensions is yet to be realized. Herein, we address this challenge by cycloaddition between C60 and an aromatic compound. The C60 layer is assembled on the well-defined molecular network, allowing appropriate molecular orbital hybridization. Upon thermal activation, covalent coupling perpendicular to the surface via [4 + 2] cycloaddition between C60 and the phenyl ring of the molecule is realized; the resultant adduct shows frozen orientation and distinct sub-molecular feature at room temperature and further enables lateral covalent bonding via [2 + 2] cycloaddition. This work unlocks an unconventional route for bottom-up precise synthesis of three-dimensional covalently-bonded organic architectures/devices on surfaces.