Given that ultrasound-assisted aqueous extraction is gaining importance within “green technology” and to increase the efficiency of extracting bioactive compounds from Levisticum officinale root waste, optimization of its parameters was undertaken. Multi-objective (multi-criteria) optimization can be an extremely promising tool not only for designing and analyzing the extraction process, but also for making process-control decisions. Therefore, the main objective of this study was to develop and optimize an environmentally friendly ultrasound-assisted extraction methodology for the aqueous extraction of bioactive compounds from the roots of Levisticum officinale, which are considered a by-product. The focus was on determining the optimal extraction conditions of the independent variables, such as solid–liquid ratio, extraction time and ultrasound power, so that the optimized extracts present the highest bioactive potential expressed in terms of levels of phenolic compounds, flavonoids, sugars and antioxidant potential. Based on the Pareto-optimal solution sets, it was found that to maximize the criteria, aqueous extraction should be carried out at a Levisticum officinale biomass/solvent ratio of 0.0643 g/mL for a time of 8.1429 to 9.0000 min, with ultrasound assistance of 162.8571 to 201.4286 W. Among the compromise solutions, the so-called “best efficient solution” was indicated as the solution for which the Euclidean distance from the ideal point of Utopia was the smallest (among all analyzed points of the collection), which had coordinates x1comp = 0.0750 g/mL, x2comp = 9.0000 min and x3comp = 214.2857 W. The results obtained will provide a valuable tool to assist in the decision-making process of controlling such an extraction process.