This study sought to investigate relationships between motivations to learn science and motivations for natural experience in junior high school students. The participants were 265 students in Kochi Prefecture, Japan. Firstly, explanatory factor analysis revealed that motivations for natural experience were composed of three factors: “familiarity with immediate natural environment”, “familiarity with animals through the senses”, and “interest in animal morphology and ecology”. Next, confirmatory factor analysis and structural equation modeling were used to further study the interrelationships. Motivations to learn science was assumed to include two factors: “expectancy of success” and “task values”. Excellent model fi t showed that factors in motivations to learn science have statistically significant effects on factors in motivations for natural experience.