Microorganism-based ecological environment monitoring technologies utilize the sensitive response of microorganisms to environmental changes, assessing environmental quality by detecting the physiological and biochemical characteristics, community structure, or functional variations of microorganisms. This approach demonstrates unique advantages in biodiversity conservation, environmental pollution prevention, and ecosystem health diagnostics. This study reviews the fundamental principles and research progress of microbial environment monitoring technologies through literature analysis. Based on patent studies, it uncovers the technological development paths and key features of advancements in this field. Combined with industry research, it evaluates the conditions for industrial development, including policy support, market demand, and technological innovation, while outlining the current state and challenges of the industry. Research indicates that microbial monitoring technologies have become important approaches to overcome limitations of traditional physicochemical monitoring, and innovations in microbial indicator methods, microbial sensors, and microbial ecology assessment are driving environment monitoring into a new phase. The development of synthetic biology technologies, environmental DNA analysis, and intelligent detection equipment has enriched monitoring methodologies, while market demand in specialized sectors continues to grow. The study recommends strengthening technological innovation and improving the standardization system for microbial genomics, constructing an industrial innovation ecosystem for microbial environment monitoring, and enhancing policy support and biosafety management, thereby promoting the high-quality development of China’s microbial environment monitoring industry.