The invention relates to a method for selecting autonomous navigation signposts of a deep space probe based on an observing matrix, which is particularly suitable for a navigation system for carrying out autonomous confirmation on the position and the posture of a deep space probe by utilizing three signposts and belongs to the field of autonomous navigation. By reading the position data of navigation signposts in a target celestial body coordinate system, position vectors of n signposts relative to the probe in the target celestial body coordinate system are calculated; by calculating a row vector of the observing matrix, an observing matrix H is obtained; the sum of characteristic values of a matrix (HHT)-1 corresponding to the combination of any three navigation signposts is calculated, and the three optimal navigation signposts are selected. The method for selecting autonomous navigation signposts of a deep space probe based on the observing matrix has high precision, less calculation and feasible analysis; and the invention provides a clear and feasible method for selecting the navigation signposts for the deep space exploration of target celestial body flight.