A nematicidal actinomycete strain WH06 was isolated from soil samples and was identified using 16S rRNA as Micromonospora sp. Through medium screening and fermentation, 10 metabolites were isolated from the ethyl acetate extract of its fermentation broth using Sephadex LH-20 and silica gel column chromatography. These compounds were identified as N-acetyltyramine (1), N-acetyltryptamine (2), 1-methylhydantoin (3), benzenepropanoic acid (4), cyclo-(L-Pro-L-Tyr) (5), cyclo(L-Phe-Gly) (6), catechol (7), methyl (4-hydroxyphenyl)acetate (8), 3-hydroxybenzoic acid (9), and 4-hydroxybenzoic acid (10). In an in vitro assay against Meloidogyne incognita, a root-knot nematode, compounds 1, 4, 9, and 10 show nematicidal activity. Among them, benzenepropanoic acid (4) causes 99.02% mortality of nematode at 200 μg mL−1 after 72 h. Moreover, compound 4 also displays activity in inhibiting egg hatching of M. incognita. This suggests that Micromonospora sp. WH06 is a promising candidate for biocontrol of M. incognita.