With stepwise development of Chinese enterprise, management problem is increasingly prominent, especially human resource management issues. Facing international environment of entering into World Trade Organization, the country accelerates construction pace of human resource management subject in colleges and universities, which provides professional channel for management efficiency and market competition ability of Chinese enterprise, but it is still far from practice. In this paper, the concept, origin and inhibition factors of ingroup preference are elaborated. Based on the visual angle of ingroup preference, started from four dimensions (enterprise incentive system, talent management idea, psychological contract and employee communication consciousness), main problems existing in employee relationship management of modern enterprise are explored. It is specially emphasized that manager often holds the blame in front of dealing with the crisis after contradiction, which is “fatal point” neglected in employee relationship management of modern enterprise. To improve its core competitive power, enterprise must value harmonious relationship with employees.