Ionic liquids (ILs) are new green solvents, which are widely used in lignocellulosic and microalgal biorefineries. However, high-temperature operating conditions limit their application in the extraction of heat-labile algal products, such as bioactive astaxanthin. In this study, we report the technical feasibility of room-temperature astaxanthin extraction from Haematococcus lacustris cysts with a thick and complex cell wall structure, by combining ultrathin α-quartz nanoplates (NPLs) with ethyl-3-methylimidazolium ([Emim])-based ILs. When four different [Emim]-based ILs with thiocyanate (SCN), diethylphosphate (DEP), HSO4, and Cl anions were applied to 90-day-old H. lacustris cysts at room temperature (~28 °C), the astaxanthin extraction efficiency was as low as 9.6–14.2%. Under sonication, α-quartz NPLs disrupted the cyst cell wall for a short duration (5 min). The astaxanthin extraction efficacies of a subsequent IL treatment improved significantly to 49.8% for [Emim] SCN, 60.0% for [Emim] DEP, 80.7% for [Emim] HSO4, and 74.3% for [Emim] Cl ions, which were 4.4, 6.1, 8.4, and 5.2 times higher than the extraction efficacy of only ILs, respectively. This finding suggests that α-quartz NPLs can serve as powerful cell-wall-disrupting agents for the room-temperature IL-mediated extraction of astaxanthin from robust algal cyst cells.