In recent years, many droughts have happened over mainland Australia, especially the two severe prolonged droughts, from 2006 to 2009 and 2018 to 2020, resulting in serious water scarcity. Therefore, using the Total Storage Deficit Index (TSDI) from the Gravity Recovery and Climate Experiment (GRACE), we analyzed the two severe prolonged droughts from the perspective of the affected area, spatial evolution, frequency, severity and drought driving factors. The results show that the affected area of Drought 2006–2009 ranged from 57% to 95%, and that of Drought 2018–2020 ranged from 45% to 95%. Drought 2006–2009 took its rise in southeastern Australia and gradually spread to the central part. Drought 2018–2020 originated in the southwest corner of the Northern Territory and northern New South Wales, and gradually expanded to Western Australia and the whole New South Wales respectively. During Drought 2006–2009, Victoria suffered drought all months, including 59% mild drought and 41% moderate drought, North Territory had the highest drought severity of 44.26 and Victoria ranked the second high with the severity of 35.51 (cm months). For Drought 2018–2020, Northern Territory was also dominated by drought all months, including 92% mild drought and 8% moderate drought, the drought severities were in North Territory and Western Australia with 52.19 and 31.44 (cm months), respectively. Finally, the correlation coefficients between the two droughts and Indo-Pacific climate variability including El Niño-Southern Oscillation and Indian Ocean Dipole (IOD) are computed. By comparing the correlation coefficients of Drought 2018–2020 with Drought 2006–2009, we find that the impact of the El Niño on the hydrological drought becomes weaker while IOD is stronger, and the role of Southern Oscillation on droughts is diverse with the quite different spatial patterns. The results from Fourier analysis confirm that the two hydrological droughts are all related to Indo-Pacific climate variability but with slightly different driving mechanisms.