An efficient ionic liquid-mediated microwave-assisted hydrodistillation concatenated liquid-liquid extraction (ILMHDE) technique was developed for distillation of essential oil and extraction of non-volatile flavonoids (astragalin, quercetin, luteolin, kaempferol and apigenin) from the inflorescences of Helichrysum arenarium (L.) Moench. In addition to collecting essential oil on the top of hydrosol in the conventional oil-water separation process, another extraction process was realized for extracting some essential oil components from the hydrosol using a small amount of organic solvents, which can effectively reduce the organic content in wastewater and its further disposal burden. Through comparison, 1.0 M [C8mim]Br was selected for the extraction and distillation in a sample reaction flask, and ethyl ether was chosen as the extraction solvent in the second separation column. Based on the yields of total essential oil and total flavonoids, the ILMHDE process parameters (liquid-solid ratio, microwave irradiation time, microwave irradiation power) were optimized via the Box–Behnken design. Due to the combined effects of the microwave irradiation, the addition of ionic liquid and the modified hydrodistillation concatenated liquid-liquid extraction apparatus, greater advantages were found in the ILMHDE process compared with other traditional methods, as evidenced by the extraction kinetics. After the GC–MS analysis, a higher content of oxy-components was detected in the essential oil that was separated in the second separation column than that in the first one, and a more valuable essential oil was achieved. Therefore, the ILMHDE technique is a good alternative for simultaneous distillation of essential oil and extraction of non-volatile components from medicinal plants.