The calculation of the meridional overturning streamfunction in the southern Indian Ocean is biased by the Indonesian Throughflow. Therefore, this study applies the vertical overturning streamfunction to diagnose the shallow overturning circulation in the Indian Ocean. Using the Ocean General Circulation Model for the Earth simulator output, improvements with the vertical overturning streamfunction compared with the meridional overturning streamfunction are explored. The results show that the vertical overturning streamfunction smoothly connects the shallow overturning circulations of the northern Indian Ocean and the southern Indian Ocean with the whole cycle of the subtropical cell and the cross-equatorial cell. The vertical overturning streamfunction shows a much cleaner shallow overturning circulation, which is underestimated by the meridional overturning streamfunction. It shows that the shallow overturning circulation has a magnitude of ~13 Sv (1 Sv ≡ 10 6 m 3 s − 1 ), of which the subtropical cell accounts for ~8 Sv. In addition, the vertical overturning streamfunction captures a clockwise overturning cell in the upper 600 m layer between 30°S and 34°S. This cell has a magnitude of about − 5 Sv and probably corresponds to the wind-forced subtropical gyre. Therefore, the vertical overturning streamfunction provides a new approach for estimating the shallow overturning circulation in the Indian Ocean.