In this paper an embedding algorithm based on commute time is implemented by organizing patches according to the graph-based metric, and its performance is analyzed by comparing with the results of principal component analysis embedding. It is usual that the dimensionality reduction be done within some acceptable approximation error. However this paper shows the proposed manifold embedding method generates the intrinsic geometry corresponding to the signal despite severe approximation error, so that it can be applied to the areas such as pattern classification or machine learning.