Provided is a method for interference alignment applied to a multi-cell and multi-user Multiple Input Multiple Output (MIMO) system. The method includes that: a BS divides multiple users in a cell into a plurality of user groups, and notifies the multiple users of grouping information; and when one of the plurality of user groups is interfered by a neighbor cell, users in the one of the plurality of user groups cooperate with each other to perform interference alignment. The disclosure also provides a pre-coding method and system based on interference alignment. The disclosure, by means of grouping and cooperation of the users and designing of a receiving matrix of each user, achieves the effect of interference alignment in a signal transmission space of the BS.