Photocatalytic H2 production is a promising way utilizing solar energy to replace fossil fuels. To develop highly efficient, earth-abundant, and low-cost cocatalysts to replace Pt is significant for the scalable solar H2 production. Herein, a lithium incorporation assisted method is developed to synthesize ultra-small Mo2C nanodots, whose cocatalytic activity is 12.23 times of the pristine MoC coupled with CdS. Morevoer, the photocatalytic performance of Mo2C/CdS measured in the lactic acid aqueous solution is 5.81 times of Pt/CdS under the same condition and 71% of Pt/CdS measured in the Na2S/Na2SO3 solution. The apparent quantum yield (AQY) at 420 nm is as high as 39%. And it shows a better cocatalytic performance than Pt loaded on g-C3N4. The high cocatalytic performance is attributed to the more exposed active surface area because of the small size and high loading amounts of Mo2C on carbon. The mechanism study suggests that the Li ion incorporation is beneficial for the formation of ultra-small MoO2 nanodots intermediate during the pyrolysis of ammonium molybdate and ultra-small MoO2 nanodots are transformed to ultra-small Mo2C nanodots accompanying with the Li ion removal after the further carbonization. It is expected that this strategy can be applied to synthesize other ultra-small metal compound nanodots.