This study aimed to study the effects of the 5Es-learning cycle using the metacognitive moves and the teacher’s handbook instruction on learning achievement, integrated science process skills and critical thinking of 82 high school (Grade 9) students from 2 classes, were selected by the use of the cluster random sampling technique. These students were randomly assigned to an experimental group who learned using the 5Es-learning cycle using metacognitive moves and a control group who learned using the teacher’s handbook instruction, 41 students each. Research instruments included, 6 plans of learning organization by using the 5Es-learning cycle with 3 metacognitive moves: intelligibility, plausibility and wide-applicability; 6 plans of learning organization using the teacher’s handbook, each plan for 3 h of learning in each week; the learning achievement test with 40 items; the integrated science process skills test with 5 subscales and 30 items and the critical thinking test with 5 subscales and 54 items. The data were analyzed by a percentage, a mean, a standard deviation and for testing hypotheses the t-test and the F-test (Two-way MANCOVA) were employed. The major findings revealed as following: The students as a whole, the male students and the female students in the experimental group showed gains in learning achievement, integrated science process skills in general and in 4-5 subscales and critical thinking in general and in 4-5 subscales from before learning (p<0.05). The students with different gender did not statistically indicate those mentioned learning outcomes differently (p>0.05). The experimental group indicated more learning achievement, integrated science process skills in general and critical thinking in general and in 3 subscales: interpretation, deduction and evaluation of arguments, than did the counterparts (p<0.05) and the statistical interactions of gender with learning model on these 3 learning outcomes were not found to be significant (p>0.05).