The shoot growth of ‘Fuji’ apple is vigorous, which causes a poor lighting condition and a high cost to prune. Prohexadione-calcium (ProCa) has been proven to regulate the shoots growth, fruits and return flowering in apple abroad but there are fewer studies on its effect on the shoot growth, fruits and return flowing in ‘Fuji’ apple in China. Moreover, the mechanism of its action is incompletely understood. So different treatments were applied as foliar sprays to dwarf self-rooted ‘Fubrax Red Fuji ’/M9-T337 trees at 3, 14, 35 and 56 DAPF (Days after petal fall). The results showed that at the end of the growing season, spraying ProCa effectively inhibited the growth of shoots compared to control and one spray of 500 and 750 mg L-1 ProCa, two sprays of 250 mg L-1 ProCa and four sprays of 250 mg L-1 ProCa showed the highest reduction. ProCa had very slight effect on yield, quality and return flowing. During the growing season, two applications of ProCa of 250 mg L-1 on 3 and 14 DAPF significantly reduced the content of GA 1+3 , IAA and ZR but increased the content of ABA in long terminal shoot leaves in at least one time point. The expression patterns of GA-regulated genes showed that ProCa down-regulated MdGA3ox transcript level at 10, 20, 30, 40 and 50 DAPF and down-regulated MdCPS, MdGA20ox, MdRGL1a, MdSLY1 transcripts in at least one time point. This study provided a valuable insight to regulate the vegetative growth of ‘Fuji’ apple and explored the mechanism of ProCa action.