Because a heterogeneous cluster relies on a heterogeneous storage system, the data needs to be divided in a multidimensionally manner when doing computation on it. Current cluster-level programming languages have no unified representation mechanisms of transmission and transposition of multi-dimensional arrays. This article describes the programming method based on multi-dimensional array types and the Parray language, which can be used to represent the complex multi-dimensional data transposition on heterogeneous clusters in a clear way. A large-scale three-dimensional FFT implementation on Tianhe 1A based on the array type programming method and Parray is also introduced. The final code is very simple but gets a good performance and scalability at the same time.