We have examined the antimalarial structure-activity relationship of a series of methoxylated chalcones (A-CHCH-CO-B) against Plasmodium falciparum (3D7 strain) using fluorescence-based SYBR Green assay. Our study has revealed that electron releasing methoxy groups on ring A and electron withdrawing groups on ring B increases antimalarial potency while the positional interchange of these groups causes a decrease. In particular, 2,4,5-trimethoxy substitution pattern at ring A provided potent analogues which were easily derived from abundantly available natural β-asarone rich Acorus calamus oil. Cytotoxic evaluation indicated that the most active compounds 27 (IC(50): 1.8 μM) and 26 (IC(50): 2 μM) were also relatively non-toxic. Furthermore, compound 12 showed excellent resistance index of 1.1 against chloroquine resistant Dd2 strain of P. falciparum.