The aim of this study was to construct Chlorella mutants deficient in chlorophyll synthesis by atmospheric pressure room temperature plasma (ARTP) mutagenesis, and screen novel algal species with very low chlorophyll content which is suitable for protein production by fermentation. Firstly, the lethal rate curve of mixotrophic wild type cells was established by optimizing the mutagenesis treatment time. The mixotrophic cells in early exponential phase were treated by the condition of over 95% lethal rate, and 4 mutants with the visual change of colony color were isolated. Subsequently, the mutants were cultured in shaking flasks heterotrophically for evaluation of their protein production performance. P. ks 4 mutant showed the best performance in Basal medium containing 30 g/L glucose and 5 g/L NaNO3. The protein content and productivity reached 39.25% dry weight and 1.15 g/(L·d), with an amino acid score of 101.34. The chlorophyll a content decreased 98.78%, whereas chlorophyll b was not detected, and 0.62 mg/g of lutein content made the algal biomass appear golden yellow. This work provides a novel germplasm, the mutant P. ks 4 with high yield and high quality, for alternative protein production by microalgal fermentation.