This paper is concerned with the modeling of flexible multibody systems by a Rayleigh-Ritz based substructure synthesis method, so that certain advantages can be accrued by using the variational approach to derive the eigenvalue problem. As with the classical Rayleigh-Ritz method, if the admissible functions used to represent the motion of the substructures are not chosen properly, convergence can suffer. This paper presents a new substructure synthesis method with superior convergence characteristics achieved by representing the motion by means of a recently developed class of functions, namely, the class of quasi-comparison functions. This improved convergence is shown to be related to improved approximation of both the differential equations and the natural boundary conditions. The theory is demonstrated by means of a numerical example.