With the continuous development of technology, traditional marketing methods no longer meet the needs of the main forces of social consumption, and people urgently need more innovative and personalized marketing strategies. E-commerce companies must develop a comprehensive customer-oriented marketing strategy based on big data and multi-channel to achieve their long-term healthy development. This paper first investigated the impact of the digital economy on e-commerce enterprises, focused on the transformation of the digital economy on the marketing model, expounded the development analysis of e-commerce in the digital economy era, and described the development trend of e-commerce marketing in the digital economy era. Then, this paper expounded the current problems faced by e-commerce enterprises, and discussed the lack of integrity, homogeneity, large-scale marketing strategies, and the lack of analysis and application of big data. After that, this paper put forward the marketing strategy of e-commerce enterprises in the digital economy era, and studied it from three aspects, namely, building a reasonable product management structure, marketing strategy based on customized marketing content, and social media marketing strategy based on information sharing. Then this paper proposed to use genetic algorithm to strengthen the marketing strategy of e-commerce enterprises. Finally, based on experiments and surveys, this paper used genetic algorithms to strengthen the construction of e-commerce enterprise marketing strategy in the digital economy, and concluded that the new e-commerce enterprise marketing strategy was 21% more satisfactory than the traditional new e-commerce enterprise marketing strategy. Through comparison, it can see that the integrity of the marketing plan of the new e-commerce enterprise's marketing strategy was 0.33 higher than that of the traditional e-commerce enterprise's marketing strategy, and the integrity of the promotion strategy was 0.34 higher than that of the traditional e-commerce enterprise's marketing strategy. After using the new e-commerce enterprise marketing strategy, the improved management structure was 0.29 higher than that of the traditional monitoring system, and the high quality of products was 0.18 higher than that of the traditional system.