Abstract: As a manifold learning method,Isomap has been widely used for making nonlinearly reduction for hyperspectral image.However,during the construction process of the shortest path graph,the boundary points,which are not noise points,have always been omitted for the consideration of the stability of the graph.Therefore,the PLS method is introduced to repair and simulate the manifold coordinates of the lost points in the shortest path graph.And the simulated manifold coordinates have been evaluated from two different aspects to verify our method.The results show that the simulated manifold coordinates agree well with the real one.It will be quite useful for further classification or visualization with low dimensional manifold image.