The invention provides an uplink channel estimation method of a large-scale MIMO system, and the method comprises the following steps: (1) modelling for a probability model of a channel through usinga Gaussian mixture model; (2) performing channel estimation through using optimal Bayesian parameter estimation; (3) giving an iterative initial value through using a hierarchical clustering algorithm; (4) solving an edge probability density function in the step (2) through using an approximate message passing algorithm; (5) iteratively solving parameters of the Gaussian mixture model through using an expectation maximization algorithm. In the method, sparse characteristics of channel gain in a beam domain are used fully, the Bayesian parameter estimation method is used, learning statistical information in advance is not needed, and compared with the conventional channel estimation based on LS, better MSE performance can be obtained.