Rare earth elements are known to alleviate heavy metal stress. However, the potential mechanisms of alleviation remain unclear. This study compared the effects of La(NO3)3 and La(NO3)3-amino acid chelates (La(Ⅲ)-AA) on growth, oxidative stress, ultrastructure, bioaccumulation and gene expression in rice. Results demonstrated that 20 mg/L La(Ⅲ)-AA can effectively ameliorate CuSO4 (50 mg/L) stress in rice by reducing oxidative stress and increasing chlorophyll content, thus promoting growth. ICP and TEM revealed an antagonistic effect between La(Ⅲ) and Cu(Ⅱ). Exogenous La(Ⅲ)-AA decreased Cu(Ⅱ) content in rice leaves, stems and roots by 55.56%, 59.46% and 26.29%, and ameliorated Cu(Ⅱ) damage by maintaining the ultrastructure of mesophyll cells. RNA sequencing identified 7020 differentially expressed genes, and 8 were validated by qRT-PCR. Indole-3-acetic acid (IAA) concentration was detected by HPLC. Correlation analysis between OsGH3.4-IAA-Expansin revealed that IAA content is negatively correlated with OsGH3.4 (r=-0.82, P <0.05), and positively correlated with Expansin (r = 0.78, P <0.05). It’s assumed that La(Ⅲ)-induced OsGH3.4 could inhibit IAA-dependent Expansin expression, thereby conferring resistance to Cu stress. This work provides novel insights into the molecular basis underlying La-induced Cu tolerance in rice.