[Objective]Meloidogyne incongnita is a soil transmission plant parasitic nematode that causes serious losses to agricultural production worldwide. Panebacillus polymyxa KM2501-1 inhibits Meloidogyne incongnita in greenhouse experiment, and could produce a variety of nematocidal volatile organic compounds. But whether its non-volatile products have nematocidal activity is still unknown. This study focused on identification of non-volatile nematocidal metabolites from Panebacillus polymyxa KM2501-1.[Methods] Strain KM2501-1 was fermented to collect supernatant. The high purity nematocidal substance was isolated and purified by silica gel column chromatography and high-performance liquid chromatography. The structure of the nematocidal substance was identified by liquid chromatography-mass spectrometry and nuclear magnetic resonance.[Results] The fermentation filtrate of Panebacillus polymyxa KM2501-1 inhibited Meloidogyne incongnita and the egg hatching of Meloidogyne incongnita. The nematocidal efficiency was 87.66% in vitro and the egg hatching inhibitory efficiency was 92.26%. The results of structural identification showed that the nematocidal active substance produced by Panebacillus polymyxa KM2501-1 was cyclo (Pro-Phe). The nematocidal efficiency of 800 mg/L cyclo (Pro-Phe) was up to 84.75% after 96 hours exposure. Microscopic observations show that the intestinal tissue of the Meloidogyne incongnita treated with the cyclo (Pro-Phe) was disordered compared with the control group.[Conclusion] The cyclo (Pro-Phe) produced by Panebacillus polymyxa KM2501-1 is a new nematocidal substance that may inhibit nematodes by destroying the nematode intestinal tract.