Ejectors can be used in Joule–Thomson (JT) cooling systems to create sub-atmospheric pressures and to recover expansion work, and thus achieve lower temperatures and higher system efficiencies. As the key components of ejector-equipped JT cryocoolers, ejectors and counter flow heat exchangers (CFHXs) have significant effects on the cryocooler performance. In order to optimize the cryocooler performance, a 1-D ejector model, a 1-D finite-element model of CFHXs and a cryocooler model are developed. Results show that the variation of the ejector entrainment ratio with the primary flow inlet temperature depends on the ejector operation modes. Two tubes-in-tube CFHXs are designed to realize heat recovery with a relatively low pressure drop along the low-pressure channel of the CFHXs. The performance of CFHX I determines the operating conditions of the ejector, and there is an optimal CFHX I length corresponding to the maximum system COP. Differing from CFHX I, the COP increases with the length of CFHX II. For the designed cryocooler with nitrogen as the working fluid, a cooling capacity of 10.89 W at 71.8 K and COP of 0.042 can be obtained, and the COP increases by 13.1% compared to the basic ideal JT cooling cycle with the same cold-end temperature. •A model of ejector-equipped Joule–Thomson cryocooler is developed.•Effects of the ejector and heat exchangers on cryocooler performance are studied.•Heat exchangers are designed to realize heat recovery with low pressure drops.•COP improvement of 13.1% can be achieved at a cold-end temperature of 71.8 K.