Paenibacillus polymyxa CP7 antibacterial substance has a significant inhibitory action on fungus, such as Peronophythora litchi. The morphology of mycelium and sporangium of Peronophythora litchi were observed under the optic microscope, the scanning electronic microscope and transmission electronic microscope. The mycelium of Peronophythora litchi treated by CP7 antibacterial substance show morphological aberrance such as irregular distorted, wizened and swelled of mycelium. It also show the expanded end of the mycelium. The cell tissue structure of mycelium is damaged that showing the incompleted cell wall and the cell membrane, the blurred cell membrane structure, incompleted external membrane structure, and the dissolved partial cell organs. The sporangium of Peronophythora litchi treated by CP7 antibacterial substance become hollow, withered and abnormal. The wall of sporangium is injuried seriously that original massiness external cell wall only remain a thin layer, original fine structure of the sporangium is disappeared. It causes the blurred cell structure, dissolved cell organs and leakage of substances of the sporangium. In addition, the antibacterial substance also causes bacterial cells releasing of phosphorus, and inhibit cell respiration rate and NADH oxidase activity.