Microalgae with a high growth rate and a carbon fixation rate present a promising potential to produce diverse renewable energy products and reduce greenhouse gas emissions. However, some microalgal species may have limited light-use efficiency and specific growth rate. To alleviate these issues, Nannochloropsis oceanica was subjected to 137 Cs-γ radiation to obtain the desired mutant with enhanced light-use efficiency and increased biomass productivity. The N. oceanica mutant ZJU700 showed a 26.7% increase in biomass productivity after nuclear irradiation at a 700 GY dosage. It was found that the mutant had a 30.2% higher oxygen evolution rate than the wild type cells. High-throughput transcriptome sequencing showed that expression of photosynthetic related genes in the mutant were much higher than in wild type cells. Expression of the psbO gene increased by 455% in mutant ZJU700, contributing to an increased oxygen evolution rate by splitting water. Three up-regulated genes, namely petC, petF, and petH, resulted in enhanced electron transport during the photoreaction process. Up-regulation of many genes involved in the Calvin cycle indicated that CO 2 fixation rate was likely to be increased to produce more carbohydrates in mutant, thereby contributing to the increased biomass productivity in mutant ZJU700.