The current research trend is not only focused on advanced techniques to intensify the extraction of bioactive compounds from plants, but also on the optimization process. The objective of this work was the implementation of the multiple criteria analysis using navigation on Pareto sets to determine the optimal parameters for the microwave-assisted extraction of Levisticum officinale WDJ Koch roots in order to obtain the maximum efficiency of the antioxidant potential of the extracts. The optimized parameters were extraction time, microwave power, and plant biomass/solvent ratio, while the evaluation criteria were based on the total phenols, flavonoids, reducing sugars, and antioxidant capacity. It was shown that the process parameters analyzed, i.e., biomass/solvent ratio, process time, and microwave power, determined the extraction efficiency of total phenolic content (TPC). A different observation was made for the analysis of total flavonoid content (TFC) and total antioxidant potential (TAA). Compared to the assessment of TFC and TAA, a completely different trend was observed for the analysis of total reducing sugars (RSC). Sets of Pareto optimal, compromise, and preferred solutions were identified that will maximize the efficiency of the extraction of bioactive compounds from biomass. Due to the determined number of Pareto optimal solutions, an approach related to the introduction of preferences in the optimization procedure was applied. It was shown that for a satisfactory level of bioactive compounds, extraction should be carried out at a maximum microwave power of 750 W. Preferred solutions were obtained for root biomass to water ratios ranging from 0.0536 g/mL to 0.0679 g/mL. The preferred optimal time for microwave-assisted water extraction ranged from 64.2857 to 85.7143 s.