The flipped classroom pedagogy has been widely used recently. Despite many researches have paid attention with the learning outcome of flipped classroom, there has been limited attention in regard to investigate the relationship between learning behavior and learning outcomes in a flipped classroom. In this paper, we proposed to investigate the influence of online learning behaviors on short-term and long-term learning outcomes in a flipped classroom. This study used Calculus and grade point average (GPA) scores to represent short-term and long-term learning outcomes, respectively. Multiple linear regression indicated that students’ online learning behavior does not have a significant effect on short-term learning outcomes, but has a significant effect on long-term learning outcomes. For applying multiple correspondence analysis, students were divided into groups according to five grade levels based on their scores. According to GPA grade level, students’ online learning behaviors had a significant effect on long-term learning outcomes for the five groups (GPAa, GPAb, GPAc, GPAd, GPAe). According to their Calculus grade level, students’ online learning behaviors had a significant effect on short-term learning outcomes for three groups (CALa, CALd, and CALe), but two groups (CALb and CALc) did not demonstrate this trend. For exploring the effects of online learning behaviors on future learning outcomes, GPA can be considered representative because the GPA was calculated for the entire academic year 2015. Students in the CALa group exhibited the highest frequency of online learning behaviors and obtained the highest GPA grade levels (GPAa and GPAb). For the CALb, CALc, CALd, and CALe groups, students with a higher frequency of online learning behaviors obtained a higher GPA grade level. These results indicate that students’ online learning behaviors have a positive effect on future learning outcomes.