The trifoliate seedlings were treated with 4 treatments including P4B0 (pH=4,B=0 μmol/L),P4B10(pH=4,B=10 μmol/L),P6B0 (pH=6,B=0 μmol/L),P6B10 (pH=6,B=10 μmol/L) to study the effects of boron on the content of various elements at different parts of trifoliate seedlings and the roots MDA,soluble protein and activities of intracellular H+ related enzymes in low pH environment. The results showed that both B deficiency and low pH inhibited the plant height,root length and dry matter accumulation of trifoliate seedlings. Adding boron under low pH (pH=4) increased the content of elements such as K,Ca,Mg,Fe,Mn and B in roots,stems and leaves,and alleviated the cation imbalance caused by excess H+. At pH=4,the MDA content in the roots of boron deficiency treatment was 4.5 times higher than that in boron,and the soluble protein was increased by 38.8%. Moreover,at low pH (pH=4),boron addition increased the activities of NADP-ME and H+-ATPase in root cells by 114.7% and 80.8%,respectively,while the activity of PEPCase decreased by 51.4%. It is indicated that boron application under low pH conditions can increase the contents of multiple elements in the roots,stems and leaves of the trifoliate roots,regulate the activities of H+ related enzymes in the cells,maintain the intracellular pH stability,and avoid the damage caused by high H+ activity.