A basic scientific problem in neural system is to know the transition mechanism from microscopic to macroscopic level.The activity at the microscopic level is based on neurons and synapses,while that at the macroscopic level includes the basic cognitive functions,such as visual and auditory cognition,and advanced cognition.There is a great difference between microscopic and macroscopic level,and the transition is still an open problem in neuroscience.Systems science and complexity research provide a new point of view and method to this scientific problem.In the paper,the mutation in neural information transfer and conversion was discussed.Based on the research examples such as visual perception,concept formation,and memory,the methods and results of the complexity research in neural system were illustrated.Several basic types of mutation in learning process were also discussed.