Defects have been known to substantially affect quantum states of materials including charge density wave (CDW). However, the microscopic mechanism of the influence of defects is often elusive due partly to the lack of atomic scale characterization of defects themselves. We investigate native defects of a prototypical CDW material 2H-NbSe_{2} and their microscopic interaction with CDW. Three prevailing types of atomic scale defects are classified by scanning tunneling microscope, and their atomic structures are identified by density functional theory calculations as Se vacancies and Nb intercalants. Above the transition temperature, two distinct CDW structures are found to be induced selectively by different types of defects. This intriguing phenomenon is explained by competing CDW ground states and local lattice strain fields induced by defects, providing a clear microscopic mechanism of the defect-CDW interaction.