Growing evidence suggests that the imbalance of Cu leads to multiorgan diseases or other adverse effects, but the underlying mechanisms remain largely unknown. Herein, we used zebrafish to uncover the mystery of organ heterogeneous responses to Cu stress and Cu(II)-dependent spine developmental injury in the early organogenesis stage. We first demonstrated that Cu(I) was distributed in the entire body, but high contents of Cu(II) were accumulated in the yolk sac and eye in normal zebrafish larvae. Cu exposure from birth to 144 hpf caused no obvious damage to Cu-metabolizing organs (liver and intestine), despite the elevated Cu(I) and Cu(II) levels. However, the spine was more sensitive to the Cu exposure. In the spine region, the Cu(I) level remained stable, whereas the level of Cu(II) significantly increased, which was highly associated with spine development injury. A significant negative correlation between Cu(II) and the spine-related parameters was identified. Moreover, cuproptosis caused spine development deformation during the early embryogenesis stage. Spine-related pathways such as somitegenesis significantly changed in the early embryogenesis period, and 5 spine-related pathways were significantly altered in the larval stage at 96 hpf. Our study suggested that Cu stress induced organ heterogeneous Cu imbalance and Cu(II)-dependent spine development injury in zebrafish.