The invention relates to the field of genetic engineering, specifically to a polygalacturonase mutant with high catalytic efficiency and a preparation method and application thereof. According to the invention, acidic polygalacturonase originated from Penicillium sp. is used as a female parent, and molecular biological techniques are employed for domain replacement and expression of the sequence of the acidic polygalacturonase; under such a condition, specific activity of the acidic polygalacturonase is increased by 11.1 times compared with wild polygalacturonase (before mutation), catalysis efficiency of the acidic polygalacturonase is increased by 33.5 times compared with the wild polygalacturonase (before mutation), and the pH value of an optimal reaction maintains unchanged. Thus, catalysis efficiency of polygalacturonase can be substantially improved, which lays a foundation for application of polygalacturonase in industrial production fields like food, fruit and vegetable processing. The invention is of important guiding significance to improvement of catalysis efficiency of polygalacturonase and other enzymes.