To gain high sensitivity of a thermal ionization mass spectrometer, the instrument was equipped with a multichannel ion counting detector designed at the IAI RAS. With  the multichannel detector, it is possible to record mass spectra with good resolution. This is important for proper identification of spectral background components and for consideration of their contribution during the isotope analysis of ultra-small samples.  The detector characteristics and the strategy of isotope trace analysis of U and Pu by the multiple ion counting technique are discussed. Examples of analytical performance of the instrument and related technique are given: the volumes of analyzed solutions are 1–10 mkL, the detection limits of Pu and U isotopes (excluding 238U) are 0.01–0.05 pg/mL, 0.2–0.5 fg of less abundant isotope is needed for one analysis.