Although thermal ionization mass spectrometry (TIMS) has been employed for the high-precision analysis of isotope ratios, direct quantification of artificial mono-nuclide in the environment is difficult by even using isotope dilution (ID) due to the coexistence of the great magnitude of natural stable nuclides or isobars. In traditional TIMS and ID-TIMS, a sufficient amount of stable Sr doped on a filament is required to realize a stable and adequate ion-beam intensity (i.e., thermally ionized beams). However, the background noise (BGN) at m/z 90, detected by an electron multiplier, disturbs 90Sr analysis at low concentration levels due to peak tailing of a significant 88Sr ion beam dependent on the 88Sr-doping amount. Here, TIMS assisted by quadruple energy filtering was successfully employed for the direct quantification of attogram levels of an artificial monoisotopic radionuclide strontium-90 (90Sr) in microscale biosamples. Direct quantification was achieved by integrating the ID quantification of natural Sr and simultaneous 90Sr/86Sr isotope ratio analysis. Additionally, the measurement amount calculated by the combination of the ID and intercalibration was corrected for the net result amount of 90Sr by subtracting dark noise and the detected amount derived from the survived 88Sr, which are equivalent with the BGN intensity at m/z 90. Background correction revealed that the detection limits were in the range of 6.15 × 10-2-3.90 × 10-1 ag (0.31-1.95 μBq), depending on the concentration of natural Sr in a 1 μL sample, and the quantification of 0.98 ag (5.0 μBq) of 90Sr in 0-300 mg/L of natural Sr was successful. This method could analyze small sample quantities (1 μL), and the quantitative results were verified against authorized radiometric analysis techniques. Furthermore, the amount of 90Sr in actual teeth was successfully quantified. This method will be a powerful tool for measuring 90Sr in the measurement of micro-samples, which are required to assess and understand the degree of internal radiation exposure.