Background: Critical thinking is an important thing possessed by the students as an order thinking skills which support independent and research-based learning for students. One attempt to fulfill the scientific learning process is conduct a project-based learning by taking into account the motivation and learning styles of students. This study aimed to identify the effect of project based learning, motivation, and visual, auditory and kinesthetic (VAK) learning styles on high school students’ critical thinking skills of the ecosystem topic. This research used quasi-experiment with 2x2x3 factorial design. Research was conducted on high school students in grade 10th in Jakarta as many as 348 students were taken by simple random sampling technique. Data was collected by a motivation and VAK learning style questionnaire and critical thinking skills test. Data was analyzed by General Linear Model Uni-variate ANOVA at α = 0.05. The whole group had a normal distributed and homogeneous data. The results showed that (1) there is the significant effect of the Project-based learning on students' critical thinking skills, (2) motivation affects students' critical thinking skills, (3) VAK learning style does not affect students' critical thinking skills, (4) the interaction between the two independent variables was fitted (learning models*motivation , learning models*VAK learning styles , and motivation * VAK learning style )and does not affect student’s critical thingking skills, and (5) interaction model of learning , motivation , and learning styles affect the students' critical thinking skills. Based on the results above, students’ critical thinking ability can be improved through the project-based learning by taking into several factors such as students’ motivation and learning styles.