Interaction between Trichoderma harzianum and cucumber Fusarium wilt pathogen was studied in vitro and in vivo. Three tested isolates of T. harzianum exhibited distinct inhibitory effects on Fusarium in dual tests. Isolate TN showed performed more inhibitively than the other tested isolates. Field inoculation of T. harzianum resulted in enhanced content of flavonoids, phenolics and lignin in cucumber plants. Meanwhile, the activities of CAD, PPO, G-POD, CA-POD and CGA-POD were increased by 100%, 54%, 278%, 143% and 52%, respectively. The expression level of resistance-related genes in plants inoculated with T. harzianum was higher than that of the control. The expression levels of all selected genes but CCOMT were higher on 6 dai (days after inoculation) than those on 2 dai. The expression levels of C4H, CAD, CCOMT, G6PDH, PAL andPR-1 in the T. harzianum colonized plants were 5.64, 5.31, 4.28, 15.33, 7.36 and 6.45 times higher than that in control, respectively. Our findings demonstrated the close relationship between secondary metabolism and the T. harzianum-mediated induced resistance towards Fusarium infection in cucumber roots.