Provided are a reconfigurable processor, which is capable of reducing the probability of an incorrect computation by analyzing the dependence between memory access instructions and allocating the memory access instructions between a plurality of processing elements (PEs) based on the results of the analysis, and a method of controlling the reconfigurable processor. The reconfigurable processor extracts an execution trace from simulation results, and analyzes the memory dependence between instructions included in different iterations based on parts of the execution trace of memory access instructions.