Microbial technologies in environmental engineering are vital for the construction of ecological civilization. This study provides a comparative analysis of research progresses and core technological pathways in four major fields: water treatment, soil remediation, waste gas treatment, and solid waste disposal. It highlights the profound transformation of the field, driven by key technological breakthroughs such as microbial metabolism regulation, functional carrier innovation, and synthetic biology applications, evolving from empirical processes to rational design paradigms, from single-strain inoculants to synergistic microbial consortia, and from localized remediation to system-level optimization. Meanwhile, it analyzes the policy drivers, market landscape, and technical bottlenecks constraining industrial development in China. To foster high-quality development and accelerate industrial applications, the study proposes future directions including the design of functional microbial communities using multi-omics, precise delivery of microbial agents via smart materials, and dynamic process optimization through digital twin systems. It also discusses strategies for building a collaborative innovation system across the technologies, industry, and market, aiming to forge a full-chain path from technological breakthroughs to industrial applications.