Megalurothrips usitatus causes significant economic losses in the regional cowpea industry in Hainan Province, China.  However, reports on M. usitatus-resistant varieties remain limited globally.  To address this gap, this study assessed the resistance of 210 cowpea germplasm resources through field experiments over two consecutive years, and comprehensively investigated the resistance mechanism of a selected resistant variety against M. usitatus.  Physiological measurements revealed that the resistant variety IZJU0044 had higher levels of total flavonoids and tannins, as well as lipoxygenase and β-1,3-glucanase activities, both before and after thrips feeding.  Thrips feeding stimulated flavonoid biosynthesis in cowpea flowers, and the contents of both constitutive and inducible luteolin in the resistant variety IZJU0044 were higher than those in the susceptible variety IZJU0120.  Laboratory toxicity tests confirmed the lethal effect of luteolin on thrips.  Moreover, thrips feeding strongly induced luteolin synthesis-related genes (chalcone isomerases, CHIs) in IZJU0044, indicating that luteolin likely conferred higher resistance to M. usitatus.  This study provides a theoretical basis for using thrips-resistant varieties in cowpea molecular breeding programs.