Abstract: Carbon emission reduction is a typical complex system engineering, and compared with general engineering, it has the characteristics of long-term, cross-regional, multi-agent, and multi-objective. Therefore, there is an urgent need to establish a highly targeted and systematically complete carbon emission reduction system engineering theory and method to guide the research and development of related emission reduction technologies and their practical applications. Based on the definitions and characteristics of carbon emission reduction system engineering, this paper systematically summarizes the five core issues: the scale of reductions, the optimal timing of reductions, the responsible parties, the methods of reduction, and the expected outcomes. It further synthesizes four critical trade-offs faced in emission reduction engineering: short-term versus long-term, regional versus global, government regulation versus market mechanisms, and development versus emission reduction. Consequently, the paper establishes the carbon mitigation “Time-Space-Efficiency-Benefit” (TSEB) coordination theory, encompassing four theoretical dimensions: time coordination, space coordination, efficiency coordination, and benefit coordination.