Twelve undescribed 2-(2-phenylethyl)chromone derivatives, including one pair of enantiomers, together with eleven known ones, were isolated from the EtOAc extract of agarwood originating from Aquilaria filaria. All structures were elucidated by spectroscopic (NMR, UV, IR, MS) methods and compared with reported data in literatures. Twenty-one compounds were assessed for α-glucosidase inhibitory activity, which showed inhibition of α-glucosidase with IC50 values ranging between 7.8 ± 0.3 to 137.7 ± 3.0 μM (Acarbose, 743.4 ± 3.3 μM; Genistein, 8.3 ± 0.1 μM). Our results expanded the structural diversity of 2-(2-phenylethyl)chromones from agarwood, and revealed the potential of 2-(2-phenylethyl)chromones as α-glucosidase inhibitors.