To evaluate the effects of a worldwide used plant growth regulator mepiquat chloride on the nutrition value and safety of seeds of transgenic Bt cotton, inorganic element components and contents in seeds of Bt cotton (Gossypium hirsutum cv. Guoxin 6) under field condition were determined using ICP-MS. In Bt cotton seeds, 54 kinds of inorganic elements were identified by ICP-MS, and 5 kinds of major elements, K, P, Mg, Ca and Na, were in range from 138.3 to 13 835.1 μg·g-1. The contents of 14 kinds of microelements were determined as in descending order of Si, B, Mn, Sr, Zn, Ni, Cu, Mo, Fe, Co, Se, V, I and Sn, in the range from 14.2 ng·g-1 to 81.7 μg·g-1. Five kinds of heavy metals were detected with the contents from 0.14 to 55.3 ng·g-1, and their order from high to low is Pb, Cd, Cr, As and Hg. Other 30 kinds of elements were also detected in Bt cotton seeds by ICP-MS, including Rb, Be, La, Ce, Pr, Nd, Sm, Gd, Ge, Rh, Ag, Sb, W, U and Y. Foliar application of mepiquat chloride significantly reduced the contents of Ca, Fe, Si, Mn, Co, Ni, Cu and I, and remarkably decreased heavy metals Pb, Cd and Cr in the cotton seeds, by 68%, 67% and 54% respectively. While mepiquat chloride did not change the contents of most major and micro elements, it heightened 8 kinds, but lowered 7 kinds of the other 30 trace elements. This research indicated that mepiquat chloride application strengthened the security regarding the cotton seed as the material of cooking oil.