Digital image data processing is mainly to input digital image data into a computer to complete the conversion of a continuous spatially distributed image model into a discrete digital model so that the computer can identify, process, and store the processing process of digital image information. Geographic information system (GIS) is a computer system that integrates multiple forms of information expression, and it integrates functions such as collection, processing, transmission, storage, management, analysis, expression, and query retrieval, which can quickly discover the spatial distribution of things and their attributes and can express the results accurately and vividly in various intuitive forms. Therefore, on the basis of summarizing and analyzing previous research works, this paper expounded the research status and significance of processing methods for digital image data, elaborated the development background, current status, and future challenges of the GIS technology, introduced the methods and principles of permutation matrix algorithm and subimage averaging method, constructed the processing model for digital image data based on GIS, analyzed the data structure and its database establishment for digital image, proposed the processing methods for digital image data based on GIS, performed the enhancement processing and calculation classification of digital image data, and finally conducted a case analysis and its result discussion. The study results show that the proposed processing methods for digital image data based on GIS can perform analogue-to-digital conversion of continuous images, complete the steps of sampling, layering, and quantization, and then encode the obtained discrete digital signal into the computer to form an in-plane collection of pixels; this processing method can also organically combine spatial information and image data and identify, process, and store digital image data from both spatial and attribute aspects. The study results of this paper provide a reference for further research on the processing methods for digital image data based on GIS.