Nannochloropsis has been considered as a promising feedstock for biodiesel production in recent years. To improve its lipid productivity, heavy-ion irradiation mutagenesis, an effectively breeding method used in plants and microorganisms was applied in Nannochloropsis oceanica OZ-1. After large-scale screening using Imaging-PAM and microplate-reader, two mutants (HP-1 and HP-2) with higher growth rate were isolated from the wild type N. oceanica. Subsequently analysis showed that after 18 days of cultivation biomass accumulation of the HP-1 and HP-2 mutant was increased by 19% and 26% respectively compare to the wild type. Total lipid productivity of the HP-1 and HP-2 mutant was 295 mg/(L·d) and 275 mg/(L·d), respectively, whereas that of the wild type was 247 mg/(L·d). Both mutants showed significantly advantage over their wild type concerning biomass accumulation and lipid productivity.