The results of comparative estimation of the accuracy of autonomous navigation of small spacecraft in formation flying are presented. To carry out the research, the “zenith” method and the method of navigation by orbital references were chosen. These methods are based on measurements of the angular position of the Earth and an orbital reference point relative to navigational stars. Assumptions concerning the central terrestrial gravitational field and the normality of errors of the on-board navigation measurements with known constant variability were introduced in the studies. The studies were carried out using the theory of analytical estimation of the accuracy of spacecraft autonomous navigation methods. The use of this theory makes it possible to obtain the covariance error matrix of the required vector of navigation parameters and to estimate the potential (maximum achievable) characteristics of the accuracy of the navigation methods used. A dimensionless navigation error coefficient was chosen as an indicator of the accuracy of small spacecraft navigation method. The coefficient is associated with the elements of the main diagonal of the covariance matrix, it characterizes the precision properties of the method, is integrated by nature and does not depend on the volume and accuracy of the results of navigation measurements. The criterion of expediency of applying the method of determining the parameters of motion of the spacecraft center of mass is based on the comparison of navigation error rates. The presented results allow us to make reasonable choice of the method of autonomous navigation and of the composition of the onboard control of small spacecraft in formation flying.