This paper elaborates the concept on organizational structure and organizational structure reform in Organizational Behavior, and describes three kinds of typical organizational structure, namely, the functional department, the divisional organization and the Matrix Structure and their advantages and disadvantages respectively. Based on the attributes and requirements of manufacture in batch production phase of civil aircraft, the paper discusses on the needs to optimize the existing organization structure of Liaison Engineering. By the systematic analysis on the liaison engineering functions and the characteristics of manufacturing by shipset in batch production phase, the proposal of shipset management is introduced to construct a matrix organization structure, so as to enhance the handling capability and efficiency of onsite engineering problems and ensure the production activity on schedule.