Underground mining of metal deposits accounts for a significant and increasing proportion in China, with mining depths continuously expanding and working conditions deteriorating. In terms of underground ventilation, the difficulty of solving the problem is increasing. Especially in mines located at high altitudes, in extremely cold conditions, and with large mining depths, the ventilation issue has always been a bottleneck in mining operations. In response to problems such as inadequate ventilation systems and insufficient fresh airflow in a complex ultra‐deep mine in Yunnan Province, an optimization strategy and research approach for ventilation systems in complex ultra‐deep mines were proposed. First, the contaminated airflow pathways in deep construction areas were redesigned to mitigate their impact on mining activities. Second, ventilation management in various production areas was enhanced to address on‐site air quality issues. Third, a visual three‐dimensional model of the deep ventilation system was constructed to establish a mutual reference framework between numerical models and on‐site conditions, enabling precise control of the ventilation system. The results indicate that after implementing the optimization measures, fresh airflow effectively reaches the working faces via designated routes, and contaminated air is efficiently channeled through planned return pathways to the main return shafts. The ventilation time after blasting is reduced from 3.2 h to 1 h, significantly improving operational efficiency, while issues such as contaminated air retention and airflow short‐circuiting are effectively resolved. This study offers technical guidance for optimizing ventilation systems in complex ultra‐deep mines and provides crucial technical support for resource extraction in kilometer‐deep mines.