This research aims at determining the effect of learning models on motivation, creative thinking skills, and cognitive learning results of students of Senior High School 6 of Ambon, Indonesia. This research is quasi-experimental research using a non-equivalent pretest-post-test control group design. The subjects of this research were class XI Science students with a total number of 40 students. One group was taught by using the Modified Problem Based Learning (M-PBL) and the other group was taught by using the discovery learning model. Research data were collected using test and non-test instruments. The data were analyzed by using ANCOVA with a significance level of 5%. The results of the analysis show that the significance value of the learning model towards students' learning motivation and cognitive learning results was 0.000<0.05. The significance value of the learning model towards students' academic skill was 0.000<0.05. The significance value of the learning model towards students' creative thinking skills was 0.030<0.05. The results of this research indicate that the implementation of the M-PBL learning model has an effect on students' learning motivation, creative thinking skills, and learning results better than that of the discovery learning model.