This study explored the relationships among parental involvement, science motivation and one-year later science achievements of the junior high school students in rural towns in Taiwan. The research subjects consisted of 425 8th grade junior high school students, including 221 males and 204 females. The mean age of the students was 14.36 years, with a standard deviation of 0.48. The parental involvement and positive parenting subscales of the Alabama Parenting Questionnaire Child Form (APQ-Child Form) as well as the Junior High School Student Science Motivation Scale were used in the study. The software IBM SPSS 18 and AMOS 20 were used for analyzing the data. The structural equation modeling (SEM) techniques were used to evaluate the hypothesized theatrical model, and a two-stage analysis strategy was applied. The fit of the measurement model was estimated in the first phase, and the fit of the structural equation model was estimated in the second stage. Moreover, multiple group analysis was applied in order to evaluate gender differences, and bootstrapping was applied in order to examine the mediation effects of science motivation. The study results offered support for the theoretical relationships among parental involvement, science motivation and science achievements. The multiple group analysis results provided support for the gender invariance of the hypothesized theatrical model, and the bootstrap results confirmed the partially mediating role of science motivation in the relationship between parental involvement and science achievements. In summary, the results demonstrated that parental involvement can impact their children’s science motivation, which in turn can improve the school’s success in science education one year later for the junior high school students living in rural towns. The findings were consistent with Coleman’s theory of social capital and provided evidence that supports Grolnicks and Slowiaczek’s motivational model. Based on the above results, some suggestions were proposed for improving students´ science motivation in rural towns.