The purpose of this study was to know about the potential effect of geogebra software on students’ mathematical thinking and to explore thinking structure in analytic geometry. To investigate geogebra effect, a sample of forty students (grade-12) of F.G Boys Inter College Mardan Cantt was selected. Further, they were divided on the basis of their grade-11 scores record into experimental and control group. Two groups with almost equal statistical background were constructed through pair random sampling and with the same compatibility in the biological age and the social background. A six week experiment of 22 lessons was prepared and two teaching methods (tradition vs geogebra aided instructions) were tested for two groups (Experimental vs Control). The data were collected through researcher made test. To find the significance means differences of the two groups, t- test was used. The study showed that there were statistically significant differences between the means of two groups of the five variables (generalization, analytical thinking, logical thinking, abstract thinking and representation).The only aspect which was found to be insignificant was the problem solving, for which the mean score of the experimental group was improved but with no statistical significance.