Strontium-90 is a major radioactive nuclide released by nuclear accidents and discharge waste. Input of such radioactive nuclide into earth surface environment causes potential threat of long-term internal exposure when taken up by organism. Rapid and precise measurement of 90Sr in variety of environmental sample is important to understand the distribution and dynamics of 90Sr in the local environment after the accident and to assess the effect of radioactive nuclide inputs on bodies. However, previous 90Sr measurement techniques have drawbacks such as long measurement times for radiometry and high detection limits for mass spectrometry. Here we present a technique to accurately measure a significantly small amount of 90Sr in natural environmental samples using an energy-filtered thermal ionization mass spectrometry. Our technique achieved a 90Sr detection limit of 0.23 ag, which corresponds to a 90Sr activity of 1.2 µBq. The detection limit was lowered by two orders of magnitude compared with the previous mass spectrometric 90Sr analyses. The ability of our technique will expand the applicability of mass spectrometric 90Sr survey not only to the rapid 90Sr survey upon nuclear accidents but also to study a long-term environmental diffusion of radioactive materials using size-limited environmental and biological samples.