Big data technology has undoubtedly accelerated the efficiency of data processing, made data become an important reference basis in enterprise operation, and changed the mode of enterprise operation as well as the existing business model. With the development of computer technology and related equipment, more and more enterprises and organizations can begin to use big data processing technology. However, many small and medium-sized enterprises, because they cannot afford the high cost of research and development and leasing, are gradually eliminated in the information-based business competition, so it is necessary to adopt certain strategies to help small and medium-sized enterprises out of this crisis. For fragmented big data obtained from different data sources, this paper adopts load-balancing technology to provide horizontal service cluster scalability and designs a separate system module for routine testing. The experimental results show that the improved big data processing system based on genetic algorithm in this paper can better meet the business needs of small and medium-sized enterprises and meet the application needs of small and medium-sized enterprises. The simulation results also show the advantages of the system in this paper, which is faster, higher accuracy, less energy consumption, lower requirements for equipment, and more suitable for small and medium-sized enterprises. This paper designs a kind of effective big data processing system by studying genetic algorithm and computer technology.