Lotus (Nelumbo nucifera Gaertn.) seeds are rich in proteins and are considered to be a beneficial source of plant proteins. In this study, lotus seed protein hydrolysate (LSPH) was prepared using Flavourzyme and antioxidant activities were evaluated. The LSPH possessed the highest DPPH-scavenging (EC50 2.9 mg/mL), H2O2-scavenging (EC50 16.1 mg/mL), and reducing power activity (8.0 mg/mL) at 180 min of hydrolysis. After gel filtration and reverse phase HPLC purification, the low molecular weight fraction was then analyzed by Nano-LC-MS/MS. Sixteen peptides with corresponding mass from 1 to 2 kDa were identified. Peptides with hydrophobic features and acidic amino acids, Asp and Glu, are considered to contribute to overall antioxidant activities. These results show Flavourzyme hydrolysis of lotus seed protein successfully generates low molecular fragments that make them a potential nutraceutical or health promoting supplement.