Blueberry is one of the most perishable fruits, and the postharvest supply chain environment temperature has great effects on fruit quality. In order to determine the critical steps referring to non-optimal conditions and the key quality indexes in response to temperature along the cold chain, 15 time–temperature scenarios were conducted simultaneously for the storage of blueberry fruits and 17 quality attributes were determined. The results indicated that different cold chain steps under abusing temperatures significantly affected blueberry qualities. Based on the comprehensive evaluation analysis, storage in farm at 8 °C and a 10 h delay in precooling were found to be the critical steps that had strong impacts on the qualities of blueberries, affecting 33 and 31 total qualities during shelf life, respectively. Furthermore, seven effective indexes, including the sensory scores, weight loss, decay rate, content of titratable acid, malondialdehyde, respiratory rate and antioxidant activities, were confirmed to be the key quality attributes influenced by the cold chain temperature. It is necessary to circulate postharvest blueberry fruits under relatively isothermal and optimum temperatures throughout the cold chain to maintain the preferred quality, especially at the initial stage of the supply chain.