Climate change is a serious problem that requires people's cooperation to solve, and it has been reported that there have been gaps in perceptions about the cause. However, little is known about what makes people perceive that climate change is human-induced, nature-induced or induced by some other factor and the linkage between perception and cooperation. We analyze the determinants of human-induced perception and the impact of the gap in perceptions on cooperative behaviors toward climate change by conducting a survey experiment with a climate donation game with 400 Japanese subjects. First, the analysis identifies the importance of people's scientific literacy in explaining the perception gaps in that those with high scientific literacy tend to have the perception of human-induced climate change. Second, people are identified as being cooperative toward climate change, as they have a prosocial value orientation, high scientific literacy and the perception of human-induced climate change, demonstrating two important roles of scientific literacy as not only a direct determinant but also an indirect one, through a mediator of people's perceptions. Overall, the results suggest that scientific literacy shall be a key to enhancing cooperation toward climate change by promoting the perception of human-induced climate change.