In this study, an ultrasonic-assisted extraction using microemulsions was developed for the recovery of natural astaxanthin from shrimp waste. To select applicable solvent systems, the phase equilibrium, microstructure, and physical properties of the microemulsions were investigated. Then the effect of ultrasonic power, ultrasonic time, and microemulsion composition on the extraction efficiency (EEAst) and extraction yield (E-Ast) of astaxanthin were determined. Compared with organic solvents (ethanol, acetone, and dimethyl sulfoxide), the microemulsion contained tributyloctylphosphonium bromide ([P-4448]Br), tributyloctylphosphonium trifluoroacetate ([P-4448]CF3COO), or tetrabutylphosphonium trifluoroacetate ([P-4444]CF3COO) resulted in significantly enhanced extraction of astaxanthin due to the stronger electrostatic interactions and hydrogen-bonding interactions. When ultrasonic-assisted extraction conditions were 50 W and 60 min, the highest EEAst and E-Ast reached 32.47 mu g.g(-1) and 99% by using the IL-in-water microemulsion of [P-4448]Br/(TX-100 + n-butanol)/water (0.13:0.25:0.62, w/w), respectively. The IL-based microemulsion is an adequate alternative to conventional methods in the extraction and recovery of astaxanthin from natural bioresources.