Organic Rankine cycle (ORC) system is considered as a promising technology for energy recovery from the waste heat rejected by internal combustion (IC) engines. However, such waste heat is normally contained in both coolant and exhaust gases at quite different temperatures. A single ORC system is usually unable to efficiently recover energy from both of these waste heat sources. A dual loop ORC system which essentially has two cascaded ORCs to recover energy from the engine's exhaust gases and coolant separately has been proposed to address this challenge. In this way, the overall efficiency of energy recovery can be substantially improved. This paper examines a regenerative dual loop ORC system using a pair of environmentally friendly refrigerants, R1233zd and R1234yf, as working fluids, to recover energy from the waste heat of a compressed natural gas (CNG) engine. Unlike most previous studies focusing on the ORC system only, the present research analyses the ORC system and CNG engine together as an integrated system. As such, the ORC system is analysed on the basis of real data of waste heat sources of the CNG engine under various operational conditions. A numerical model is employed to analyse the performances of the proposed dual loop cycle with four pairs of working fluids. The effects of a regenerative heat exchanger and several other key operating parameters are also analysed and discussed in detail. The performance of the integrated engine-ORC system is then analysed under actual engine operating conditions which were measured beforehand. The performance of the proposed system under off design conditions has also been analysed. The obtained results show that the proposed dual loop ORC system could achieve better performance than other ORC systems for similar applications. (C) 2017 The Authors. Published by Elsevier Ltd.