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.