Mobile Augmented Reality (MAR) is considered to be a promising tool in science classes to foster kids’ imagination. In this paper, a parametric simulation method of DNA three-dimensional structure is proposed for middle school biology class. Affine transformation was used to stack and spiral complementary paired nucleotides in three-dimensional space according to the structural parameters of different DNA conformations. The process of vector construction was dynamically simulated by the recognition technologies (i.e., image characteristics and collision detection). The prototype system was developed using mobile technologies, which combines multiple interactive methods (i.e., viewing, listening, touching, and physical objects) to provide users with an appropriate learning and cognitive way. The system is useful for learners (especially K−12 students) to utilize the fragments of spare time outside the class to promote the cognition of DNA. In the future, such technology-assisted education would be a popular open learning form.