This study aims to determine the effect of learning models on high-order thinking and science process skill of students at ecology topic in class X SMA Negeri 1 Kuala. The research applied experimental quasy method with 3 classes choosed by using cluster random sampling technique. The class X-2 learn with Problem Based Learning, class X-4 with Guided Discovery, and while class X-1 with Direct Instruction models (control). The research instruments were learning outcome test in multiple choice form for higher order thinking and essay test for science process skills. The data analysis technique used Covariate Analysis (Anacova). The research results showed that there was significant effect of learning model on students' higher order thinking (Fcount = 4.371; P = 0.039). The student higher order thinking that learn by Problem Based Learning (86.55 ± 4.0) was significantl highest than Guided Discovery (83.83 ± 3.3) and Direct Instruction models (80.61 ± 3.1). There was also significant effect of learning model on students science process skill (Fcount = 6.106; P = 0.015). The students science process skills learn by Problem Based Learning (85.50 ± 4.2) was significant highest than Guided Discovery (83.31 ± 4.4) and Direct Instruction models (81.26 ± 3.1). The research result recommends the implementation of Problem Based Learning model in order to improve the higher order thinking and science process skills of the students at ecology topic in biology instruction.