The purposes of the study were: (1) to understand junior high school students´ misconceptions in learning geometry; (2) to analyze students´ cognitive process in constructing geometry concept; (3) to design an appropriate teaching strategy program for junior high school students to improve their misconceptions in geometry; and (4) to examine the effects of the teaching strategy program with integrated cooperative learning on students´ concept in geometry learning. The research instruments in the study included Geometry Test, Motivational Belief Inventory, and Metacognition Inventory. The study was divided into two parts. The first part was to explore the students´ misconceptions in learning geometry with the use of qualitative analysis. The second part was to examine the effects of taching strategy program with integrated cooperative learning by means of empirical study. The collected data were analyzed by triangulation, one-way ANCOVA, and one-way MANCOVA. The results were as follows: (1) Junior high school students students have systematic misconceptions in geometry learning. (2) There were differences between novice and expert students in geometry concept thinking modes, and there were differences between teachers and expert students, too. (3)After the experimental group accepted the teaching strategy program, the subjects of Experimental Group had higher scores on Geometry Test than those of control group. (4) The subjects of experimental group had higher scores on self monitoring and self evaluation than those of control group. (5) There were differences on executive control and motivational belief between experimental group and control group. Based on the findings, the study suggested that the teachers should use integrated cooperative learning in teaching geometry to help the students know the methods of individualized learning, competetive learning and cooperative learning, and to help them construct correct geometry concepts.