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Abstract Previous studies have shown that solar flares can significantly affect Earth's ionosphere and induce ion upflow with a magnitude of ∼110 m/s in the topside ionosphere (∼570 km) at Millstone Hill (42.61°N, 71.48°W). We use simulations from the Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model (TIEGCM) and observations from Incoherent Scatter Radar (ISR) at Millstone Hill to reveal the mechanism of ionospheric ion upflow near the X9.3 flare peak (07:16 LT) on 6 September 2017. The ISR observed ionospheric upflow was captured by the TIEGCM in both magnitude and morphology. The term analysis of the F‐region ion continuity equation during the solar flare shows that the ambipolar diffusion enhancement is the main driver for the upflow in the topside ionosphere, while ion drifts caused by electric fields and neutral winds play a secondary role. Further decomposition of the ambipolar diffusive velocity illustrates that flare‐induced changes in the vertical plasma density gradient is responsible for ion upflow. The changes in the vertical plasma density gradient are mainly due to solar extreme ultraviolet (EUV, 15.5–79.8 nm) induced electron density and temperature enhancements at the F₂‐region ionosphere with a minor and indirectly contribution from X‐ray (0–15.5 nm) and ultraviolet (UV, 79.8–102.7 nm).