Minority areas are generally backward areas with lagging economic development level, low level of industrial structure and obvious dual structure characteristics, but these areas often contain rich natural resources and unique national culture, so it is of great significance to explore the path of upgrading industrial structure in minority areas. The article firstly introduces the input-output analysis method and constructs a multi-objective evolution model of industrial structure adjustment in ethnic minority regions from the perspectives of low carbon, employment and economy, and solves the model by using the multi-objective genetic algorithm with improved genetic operation (I-NSGA-II). Using the method proposed in this paper to carry out comprehensive and detailed quantitative calculations and effect analysis on the industrial structure of ethnic minority areas, the influence coefficient of computers, audio-visual equipment, communication equipment, and cultural and office supplies machinery is larger as an industry with higher scientific and technological content, and each increase in one unit of production has a larger pulling effect on all other sectors, and it is considered that low-carbon development, economic growth and promotion of employment are equally important. Minority areas can upgrade their industrial structure in the aspects of strengthening basic agriculture, upgrading traditional industries and accelerating the development of service industry.