The shape of fruit apex is critical to appearance quality in cucumber (Cucumis sativus L.), of which the genetic basis was poorly understood, and the use of marker-assisted breeding for fruit apex improvement is not available yet. In this study, the variation of fruit apex in different cucumber ecotypes was evaluated by fruit apex angle (variation coefficient from 7.1% to 15.7%) and fruit apex index (variation coefficient from 8.8% to 22.6%). Fruit apex associated QTLs were mapped by using 145 F2:3 families and 155 F2:6 population that were derived from the cross of different ecotype cucumbers. Phenotyping of the mapping populations were conducted in four experiments in 2 years. Four major-effect QTLs, Bfal4.1, Bfai4.1, Bfad6.1 and Bfai6.1 were consistently and reliably detected across two environments which could explain 11.6% - 33.6% phenotypic variations (R2) in the F2:3 families. Three major-effect QTLs, Ofai4.1 (R2 = 13.4%–15.5%), Ofal4.1 (R2 = 10.7%–12.8%), and Ofad6.1 (R2 = 11.6%–12.4%) were stably detected in the F2:6 population in two experiments. Bfai4.1, Bfal4.1, Ofai4.1 and Ofal4.1 were integrated to be consensus QTL fa4.1, within which 11 candidate genes were predicted. Bfai6.1 and Bfad6.1 were integrated to be consensus QTL fa6.1. QTL interaction analysis showed that Bfai6.1 has epistatic effect with Bfai4.1. This study revealed two reliable major-effect fruit apex related QTLs across multi-genetic backgrounds and environments in cucumber. The possible candidate genes regulating the shape of fruit apex, and the relationship between cell division and fruit apex morphogenesis were discussed.