With the rapid growth of curriculums in colleges and universities and the number of students,automatic course arrangement method based on calculation algorithm has become an important issue of algorithm design and research. Based on Genetic Algorithm, a new binary encoding mechanism and classroom position filling method is put forward, which is applied to improve the load and efficiency of course scheduling system. In accordance with the ratio of weights in Fitness Function, this method abandons the way of random search, directionally and randomly generates chromosomes, simplifies the quantity of chromosome information, greatly shortens the running time of the system. In the aspect of management mechanism, user intervention is introduced,dealing with initial population with high proficiency and eliminating conflicts. Data from simulation experiment proves the astringency and high efficiency of this method. Moreover, the whole design of the system applies programming technology based on container, realizing the convenient processing of uncertain data.