Abstract: This paper introduces a new scheme of three-dimensional variational assimilation(GRAPeS-3DVAR), which is suitable for a grid-point model.The domain includes China area on horizontal dimension and 15 mandatory levels on vertical dimension.The scheme adopts stream function,unbalanced potential velocity,unbalanced geopotential heig htand humidity as analysis variables which are independent of each other.The cost function takes the way ofincremental method.To solve the problems that B-1 are il-conditioned and too large to be computed,the background termis preconditioned using a sequence of variable transform,which improves the convergence in the minimization process and avoids to calculate B-1 directly.EOF decomposition is used as vertical component of analysis variable transform to project onto vertical modes and separate each three-dimensional field into two-dimensional field.Recursive filters is used as horizontal component of analysis variable transform. LBF GS method is used on solution of optimization.Simple geostrophic balanced relationship is used.The system has passed verifications strictly and proved to be credibility.In order to test the functions of the system,A series ofidea experiments were made.The results showa reasonable relationship among the multi-variables and a fast convergence in the minimized process.