The fingerprint image pre-processing is a very important part of Automatic Fingerprint Identification System(AFIS). It includes such processes like normalization，orientation filtering，binarization，thinning，etc. The fingerprint image pre-processing algorithm is complex with plenty of computation. This study designed a new fingerprint image pre-processing method by using System On Programmable Chip(SOPC) technology，realized the most of time-consuming processes by using Field Programmable Gate Array(FPGA)，and implemented the part of less time-consuming but handling complexly with the software. The soft-core Nios II processor which had been downloaded to FPGA was responsible for running the software and coordinating the software with hardware．Experimental results showed that this method could improve the quality of images and processing speed greatly，thus it ensured the real-time of AFIS and provided a new design thought for the study of AFIS.