Frequent fluctuations of CNG engine operating conditions make the waste heat source have uncertain, nonlinear, and strong coupling characteristics. These characteristics are not conducive to the efficient recovery of the DORC system. The systematic evaluation of the CNG engine waste heat source and the comprehensive performance of the DORC system is conducive to the efficient use of waste heat. Based on the theory of internal combustion (IC) engine thermal balance, this paper analyzes the dynamic characteristics of compressed natural gas (CNG) engine waste heat energy under full operating conditions. Then, based on the operating characteristics of the dual loop organic Rankine cycle (DORC) system, thermodynamic models, heat transfer models, and economic models are constructed. The dynamic response characteristics analysis and energy, exergy, and economic (3E) evaluation of the DORC system under full operating conditions are carried out. The results show that the maximum values of net power output, heat exchange area, and the minimum values of EPC (electricity production cost) and PBT (payback time) are all obtained under rated condition, which are 174.03 kW, 25.86 kW, 37.54 kW, 24.76 m2, 0.15 $/kW·h and 3.46 years. Therefore, the rated condition is a relatively ideal design operating point for the DORC system. The research in this paper not only provides a reliable reference for the comprehensive analysis and evaluation of the performance of the DORC system, but also provides useful guidance for the selection of appropriate DORC system design operating points.