Reduction of chlorophyll size has great advantages on improving the photosynthesis efficiency as well as the photolysis algal H-2 production. To promote the H-2 production, Chlamydomonas reinhardtii was mutated by atmospheric and room temperature plasma (ARTP). After the selection, an algal mutant was observed to have 1.8-5.2 times (28.5-84.1 mL L-1) and 2.7-3.1 times (356.5-405.2 mL L-1) higher H-2 production than wild-type during the algal subcultures grown in pure and co-cultures, respectively. In comparison with wild-type alga, the mutant grew as lighter green colonies on agar plate, with about 2 times larger cell diameter and 5.3-6.1 times lower chlorophyll content per unit cell volume. Results from the comparative transcriptomic analysis indicated that most of the genes relating to photosynthesis (photosystem I, II, cytochrome b6/f complex, photosynthetic electron transport, and F-type ATPase) and LHC proteins were have higher expressions in mutant cells, suggesting the improvement of photosynthesis efficiency.