Abstract: In this paper, the thermodynamic performance of an ammonia-ammonia cascade refrigeration system was systematically analyzed using both conventional exergy analysis and advanced exergy analysis methods. The ammonia-ammonia cascade refrigeration system is widely used in low-temperature industrial processes and cryogenic storage fields due to its superior low-temperature refrigeration capacity, good environmental compatibility, and high operational stability. Exergy analysis, as an effective tool for evaluating the thermodynamic irreversibility of energy conversion and utilization systems, can not only quantify the energy quality loss but also accurately reveal the location, magnitude, and intrinsic causes of exergy destruction in each unit component at the quantitative level, thereby clearly defining the optimization objectives and priority directions of each component. Through detailed quantitative calculation and in-depth mechanism analysis, the exergy destruction of each unit component in the system was accurately measured, and the key factors leading to exergy loss were comprehensively explored. The analysis results show that the high-temperature compressor, intermediate heat exchanger, evaporator, and low-temperature compressor are the main components causing the system’s total exergy destruction, and their exergy loss accounts for a major proportion of the total system exergy destruction. Further quantitative statistics indicate that the endogenous exergy destruction of the system accounts for 81.02% of the total exergy destruction, while the avoidable exergy destruction accounts for 51.15% of the total. These findings fully demonstrate that the irreversible energy loss of the ammonia-ammonia cascade refrigeration system is mainly derived from the inherent irreversible heat transfer and compression processes inside each unit component, which are the core sources of the system’s thermodynamic irreversibility. Moreover, the high proportion of avoidable exergy destruction also indicates that the main components with high exergy loss still have significant potential for energy conservation and performance improvement. This study provides a comprehensive understanding of the thermodynamic characteristics and exergy loss mechanism of the system, and offers targeted theoretical guidance for its subsequent optimization design and energy-saving transformation.