Adenosine triphosphate (ATP) is the molecular unit of intracellular energy and it is the product of oxidative phosphorylation of cellular respiration uses in cellular processes. The study explores the growth of the misconception levels amongst the learners and evaluates the effectiveness of animation model over traditional methods. The data obtained from the sixty B.Sc. students found the growing misconception status in the mitochondrial oxidative phosphorylation test. Euclidean Distance Formula was used to analyzing and interpreting the various growing misconception levels among the students and found that 88% of students have different types of misconception those were rooted in preconception derived from everyday experiences of students. Similarly, Chi-Square test used to observe the effects of the animation model over the "correct" and "misconception" status of the students and it was resulted that misconception levels relatively decreased from 88% to 15%, and only 15% of students have the misconception problems. However, Univariate Analysis of Variance used to measure the effectiveness of animation model of mitochondrial oxidative phosphorylation over the control group. It results that F[subscript (1/118)] 323.42 P < 0.01) was significant and there existed significant difference in between control and experimental group achievement of ATP generation of mitochondrial oxidative phosphorylation.