The distribution of the precipitates on the grain boundaries in Fe-3%Si steel during secondary recrystallization annealing were studied using high-angle annular dark filed (HAADF) scanning transmission electron microscopy (STEM). Because HAADF image can show both grain boundaries and precipitates clearly, the change of precipitate distribution on grain boundaries can be quantitatively analyzed. It was observed that the total area of the precipitates on grain boundaries increased in the order of non-annealed, 600°C, and 900°C sample and the total area of precipitates on grain boundaries in the 1000 °C sample was much lower than that in the 900 °C sample. The compositions of the precipitates were also analyzed using X-ray energy-dispersive spectrometer (XEDS). The most precipitates were multi-phase ones, mainly composed of AlN and MnS. Our analysis results suggest that such a precipitate behavior is responsible for the abnormal grain growth of Fe-3%Si steel occurring under the temperature above 900 °C.