Jerusalem artichoke is tolerant to various environmental stresses. Jerusalem artichoke is an alternative as feedstock for biorefinery. The GA3/ABA and IAA/ABA were greater in NY-1 than QY-2 before tuber initiation. The GA3/ABA and IAA/ABA in QY-2 surpassed NY-1 during the tuber growth stage. A dynamic balance of endogenous hormones was important for tuber development.