When the method of moment is employed to analyze large slotted waveguide arrays,filling the impedance matrix and solving the matrix equation are very time consuming.In this paper,a load balancing parallel scheme is first presented to accelerate the filling process.Then,a novel preconditioner -SN (slot neighbour) preconditioner is introduced which boosts the advantage of giving adequate consideration to the near field interaction between basis functions when the preconditioning matrix is generated.Numerical results demonstrate the validity and efficiency of the proposed algorithms and show that the SN preconditioned CG (conjugate gradient) can significantly accelerate the solution by an order of magnitude for large slot arrays.