To study the effects of different incidence stages of sesame stem rot on individual plant yield, this study investigated the growth of shattering-resistant sesame variety 'Yuzhi NS610' under natural incidence conditions. The results showed that the per-plant yield loss rate was significantly correlated with the incidence stage: no yield was obtained when the disease occurred before the early full-bloom stage; yield decreased by 82.55% at the middle full-bloom stage, 39.04% at the late full-bloom stage, and 32.96% at the final flowering stage. With delayed incidence, the reduction rates of plant height, effective capsules and fruiting nodes gradually decreased. Compared with incidence at the final flowering stage, these three reduction rates at the middle full-bloom stage showed significant or extremely significant differences. There was no significant difference in 1000-grain weight reduction rate among different stages. Decreases in fruiting nodes, capsules and effective capsules were key factors for yield loss; the influence of plant height, 1000-grain weight and other factors on yield loss varied with incidence stages.