To reduce the complexity of program comprehension such as program standardization and program matching, a program comprehension oriented construction algorithm of system dependence graph is proposed. This algorithm can be divided into three stages: program information extraction, control dependence sub-graph construction and data dependence sub-graph construction. Control dependency and data dependency are independently computed. Data flow is directly analyzed based on control dependent sub-graph without extra control flow graph, and computed on demand, which reduces the algorithm complexity. Selection statements and loop statements are uniformly represented, and expressions are represented as abstract syntax trees, which can facilitate program transformation and analysis. The system dependence graph has been used in automatic grading system of student programs and program recognition. Application results show that it can facilitate program comprehension and analysis and reduce the complexity of program comprehension and analysis.