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This paper proposes a heterogeneous data integration method based on object mapping to solve the problem of mass of heterogeneous data existing in online application of science and technology programs. Based on specific data standards, this method organizes data into tree models through aggregation of logic, describes the file structures of different science and technology programs through redefining the pruning of the models, and takes the path of a data item in the model as the sole mark of the data item, thus screening the heterogeneity of data. It lowers the cost for maintenance and management of scientific and technological data and realizes data integration and unified management. This method finds applications in the actual integrative managing environment of science and technology programs.