Although triple-quadrupole inductively coupled plasma-mass spectrometry (ICP-MS/MS) has become an attractive technique for the measurement of long-lived radionuclides, the abundance sensitivity, isobaric and polyatomic ions interferences seriously restrict the application. The spectral peak tailing and uranium hydrides (UH+, UH2+) from 238U have a serious influence on the accurate measurement of 239Pu and 240Pu, especially for the ultra-trace level plutonium isotopes in the higher uranium sample. A new method was developed using ICP-MS/MS measurement in mass-shift mode with collision-reaction gas combined with a chemical separation procedure. As O2 readily converted Pu+ ion to PuO2+, while disassociated the interfering diatomic ions of interfering elements (U, Pb, Hg, Tl, etc.), the interferences from these elements were completely eliminated if plutonium was detected as PuO2+ at the m/z more than 270. By the mass filter in MS/MS mode combined with O2 as reaction gas the lower peak tailing of 238U+ (<5 × 10−12) was significantly suppressed. By this way, the 238UO2H+/238UO2+ atomic ratio was reduced to 4.82 × 10−9, which is significantly lower than that of other collision-reaction gas modes. Interferences from Pb, Hg and Tl polyatomic ions were also completely eliminated. Thus, accurate measurement of ultra-trace level 239Pu in high uranium sample solutions with the 239Pu/238U concentration ratio of 10−10 was achieved by the mass-shift mode with 0.15 mL/min O2/He + 12.0 mL/min He as collision-reaction gas, and high elimination efficiency of uranium interferences up to 1014 can be obtained by combination with the chemical separation using a single UTEVA resin column. The developed method can be applied to accurately determine the fg level 239Pu in high uranium samples, such as large-size deep seawater, deep soil and sediment, uranium debris of nuclear fuel.