In recent years, biochar has attracted considerable attention for soil quality improvement and carbon sequestration due to its unique physicochemical properties. However, the mechanism by which biochar application negatively affects the growth of crop seedlings has not been fully investigated. In this study, a hydroponic experiment was conducted to evaluate the response of rice, wheat, and corn seedlings to biochar application (CK, 0 g/L; BC1, 0.5 g/L; and BC2, 1.0 g/L). Compared with the CK treatment, the BC1 and BC2 treatments decreased the fresh shoot and root weights of rice and corn seedlings (P < 0.05), but there was no significant effect on wheat seedlings (P > 0.05). For the contents of nutrient elements in seedlings, both BC1 and BC2 treatments hindered the roots from absorbing Fe and Cu and increased the uptake of Ca and Mn. Compared with the CK treatment, the translocation factor (TF) values of Ca, Mn, and Zn were significantly decreased especially in rice seedlings (35.3%-36.8%, 68.7%-76.5%, and 29.8%-22.0%, respectively) under the BC1 and BC2 treatments, while only Mn was significantly decreased in wheat and corn seedlings (P < 0.05). Transmission electron microscope (TEM) analysis of root cross-sections showed that nano-sized biochar particles (10∼23 nm) were found in the root cells under BC2 treatment conditions. Our findings reveal that a large amount of biochar application can reduce nutrient absorption and translocation, and hinder rice, wheat, and corn seedlings, particularly rice seedling, in hydroponic system.