When traditional methods integrate popular science microanimation works, the integration effect of the animation works is not good. In this paper, we propose an automatic integration algorithm of popular science microanimation works in the context of new media. The system first analyzes the characteristics of the new media context and gives the meaning of microanimation in the context of new media. It simplifies the edge folding of popular science microanimation integration and calculates the Facial Animation Parameter (FAP) value to realize the automatic integration of popular science microanimation works. We conducted a number of experiments using various size datasets to test the proposed system. We achieved an average integration accuracy of 96.3% with datasets of 500 to 3000 animation works, having the highest accuracy of 99% with a dataset of 500 animation works. On the other hand, the integration time of the animation works was recorded just 1.25 seconds with a dataset of 3000 animation works which is much lower than the existing work.