Citrus microcarpa is a popular nutritious fruit that is widely cultivated in China. In recent years, many compounds with significant pharmacological activities have been isolated successfully from the pericarp of C. microcarpa. However, to date, there are no reports on the activity of C. microcarpa pericarp against root-knot nematodes. This study used the ethanolic extract from the pericarp of Hainan C. microcarpa and the impregnation method to determine its activity on J2 Meloidogyne enterolobii specimens and on single-egg hatching. The results showed that when J2 individuals were treated with 50 mg⋅mL–1 of the extract, the lethal concentration 50 values after 24 and 48 hours were 17.124 and 8.858 mg⋅mL–1, respectively. The mortality rate of nematodes after 48 hours of treatment was 100%, and the inhibition rate of single-egg hatching after 24 hours was 89.29%. The ethanolic extract of C. microcarpa peels showed high inhibitory and lethal activity against the M. enterolobii. The analysis of the chemical composition of the extract revealed 28 substances with insecticidal and antibacterial effects, including lignans, flavonoids, fatty acids, organic acids, terpenoids, and imidazole. The formulas of the chemical structures and pharmacological effects of these potential insecticidal and antibacterial substances were elucidated to provide a scientific basis and a theoretical reference for the use of C. microcarpa pericarps as a raw material for the development of new, natural plant nematicides.