In our previous study, we demonstrated that the ethanol extracts of Artemisia dubia (A. dubia) and Aster scaber (A. scaber) have anti-nosemosis activity. In our present study, we intend to establish the anti-nosemosis activity of aqueous, ethyl acetate (EA), and butanol (BuOH) extracts of A. dubia and A. scaber. In order to determine the optimal dose, we performed both in vitro and in vivo toxicity for all the extracts and also carried out anti-nosemosis experiments. Although all of the extracts (aqueous, EA, and BuOH) showed in vitro and in vivo anti-nosemosis activity in a dose-dependent manner, the aqueous extracts of A. dubia and A. scaber showed more potent anti-nosemosis activity than the EA and BuOH extracts. Moreover, an aqueous extract of A. dubia + A. scaber demonstrated stronger anti-nosemosis activity compared with the aqueous extracts of either A. dubia or A. scaber alone. Although the main ingredients in A. dubia and A. scaber remain unclear, our results suggest that the active components of A. dubia and A. scaber could dissolve in the aqueous fraction.