The present invention provides an input data control method and system for a data processing system. The system comprises at least one basic operation unit (BOU) and is used for transforming one input matrix X into data in a plurality of specified columns in an output matrix Y via an inverse discrete cosine transform procedure. The method generates and outputs a transform control signal together with the input matrix to at least one of the BOUs. A new transform control signal is generated according to the received transform control signal, and outputted together with the input matrix X, to other following BOUs. The step of generating the new transform control signals is repeated until each specific column of the output matrix Y is decoded by a corresponding BOU. A basic operation procedure is then performed, and the received input matrix is decoded to obtain the data in the specified columns corresponding to the transform control signal.