Quantum states induced by single-atomic-impurities are the current frontier of material and information science. Recently the spin-orbit coupled correlated kagome magnets are emerging as a new class of topological quantum materials, although the effect of single-atomic impurities remains unexplored. Here we use state-of-the-art scanning tunneling microscopy/spectroscopy (STM/S) to study the atomic indium impurity in a topological kagome magnet Co3Sn2S2, which is designed to support the spin-orbit quantum state. We find each impurity features a strongly localized bound state. Our systematic magnetization-polarized tunneling probe reveals its spin-down polarized nature with an unusual moment of -5uB, indicative of additional orbital magnetization. As the separation between two impurities progressively shrinks, their respective bound states interact and form quantized molecular orbital states. The molecular orbital of three neighboring impurities further exhibits an intriguing splitting owing to the combination of geometry, magnetism, and spin-orbit coupling, analogous to the splitting of the topological Weyl fermion line12,19. Our work demonstrates the quantum-level interplay between magnetism and spin-orbit coupling at an individual atomic impurity, which provides insights into the emergent impurity behavior in a topological kagome magnet and the potential of spin-orbit quantum impurities for information science.