The invention provides a non-orthogonal pilot frequency distribution method for a decellular large-scale MIMO system. The method comprises the following steps: acquiring a channel large-scale fading coefficient from a user to each base station within a certain range, and calculating a coefficient ratio of the channel large-scale fading coefficient of the user to each base station to the sum of thechannel large-scale fading coefficients of the corresponding user to all base stations; according to the coefficient proportion, selecting that the sum of the minimum number of coefficient proportions of each user is greater than a certain scale factor, and taking the base station corresponding to the selected coefficient proportion as a base station group of the user; obtaining an undirected graph according to the base station group of each user, dyeing the undirected graph by adopting a graph theory vertex dyeing theory, and updating a dyeing result according to a judgment mechanism; and distributing the non-orthogonal pilot frequency of the system according to the obtained dyeing result. The method provided by the invention can effectively reduce the influence of the pilot pollution effect, improve the user capacity of the system, and improve the robustness of the pilot distribution result.