Copper (Cu) toxicity has a deleterious effect on plant growth, and different nitrogen (N) forms have significantly different impacts on the uptake and accumulation of heavy metals by plants. However, it remains unclear how excess Cu inhibits the growth of rice seedlings under different N forms. Here, we examined the mechanism of Cu toxicity inhibiting the growth of rice supplied with different N forms. Rice seedlings were grown in a nutrient solution with 0.81 mmol L-1 N, as ammonium (NH4+), nitrate (NO3-) and NH4+ + NO3-, or without N (0 N) in the presence of 0.2 mu mol L-1 CuSO4 or 10 pmol CuSO4. The inhibition of shoot growth under excess Cu was more pronounced in plants that were supplied with NO3- than NH4+; such inhibition was not induced by higher Cu concentration in shoots. Applied with NO3- alone increased solution pH value up to 6.2, but supplied with NH4+ alone and NH4+ + NO3- decreased solution pH value to 4.0 and 4.2, respectively. The increment of solution pH reduced Cu concentration in shoots of rice supplied with NO3- alone. Copper toxicity decreased NO3- concentrations in rice seedlings that were supplied with NO3- alone but increased the NH4+ concentrations in plants that were supplied with NH4+ or NH4+ + NO3-. High Cu levels reduced the uptake of NO3- in roots by the analysis of net NO3- flux and NO3- assimilation enzymes activity. Under excess Cu, the transcript levels of OsNPF6.5, OsNPF2.2 and OsNPF2.4 genes were suppressed, while OsNRT2.1, OsNRT2.2 and OsNAR2.1 were raised in roots. In conclusion, Cu toxicity inhibits NO3- uptake and upward translocation by modulating the expression level of NO3- transporter genes. The reduction in the concentrations of NO3- and total N decreased shoot growth of rice seedlings when N was supplied as NO3-. Hence, rice seedlings supplied with NO3- had lower shoot biomass than those with NH4+ under Cu stress.