The invention provides a rice fingerprint constructing method. The method includes: extracting rice genome DNA, screening SSR fluorescent primers with high polymorphism, subjecting the rice variety DNA to PCR amplification, detecting the PCR product by utilization of capillary gel electrophoresis, analyzing data to obtain a 0-1 matrix graph and converting the 0-1 matrix graph into a fingerprint mode mapping. By adoption of the characteristics of the SSR polymorphism and the high resolution of the capillary gel electrophoresis technology, the method can recognize two polymorphism bands with a band difference being 1 bp. The method is prone to automation, simple in operation, stable and reliable in results, and prone to large-scale multi-batch data integration and analysis, and is suitable for construction of a large number of rice variety fingerprints.