Thermal ionization mass spectrometry (TIMS) was used to directly quantify an ultratrace of radioactive 90Sr in microliter droplet samples. No chemical separation was required in removing isobaric interferences on M = 90 such as 90Zr and organic molecules in the mass spectrum because the difference in evaporation and ionization (emission) temperature among organic molecules, Zr and Sr, allows us to control the emission manner and significantly suppress the isobaric interferences. Direct quantification was achieved by improving the intercalibration of Faraday cups and ion counting in an isotope dilution (ID) method. Furthermore, the use of a total evaporation method (TE) enhanced the detection efficiency by the complete collection of the 90Sr ion beam from the samples and minimized the complexity of the fractionation effect in the isotope ratio calculation. In this study, 1 fg of 90Sr (equal to activity of 5 millibecquerel (mBq)) in a very low-volume sample with 108 times greater isobaric interference from 90Zr was successfully measured using the proposed ID-TE-TIMS method. The limit of detection was 0.029 fg (equal to 0.15 mBq) without any preconcentration. To demonstrate the wide usability of this method, low-volume samples of tears, eyelashes, saliva, environmental standards, and water samples (i.e., seawater and ground water) were analyzed within 1 h. The relationship of the measured values between this ID-TE-TIMS method and a radiometric analysis was shown to have good linearity.