To accurately assess the heat transfer performance of a medium-depth coaxial casing heat exchanger, this study introduced the concepts of the annual stabilized mining stage and the effective thermal influence distance for each layer of non-homogeneous thermal storage. The study area was stratified into six layers based on the geothermal temperature gradient fitting results. The findings revealed that the maximum injected circulating fluid temperature for the mid-depth coaxial casing geothermal system was 37 °C, with a maximum mass flow rate of 16.67 kg/s. When the injected circulating fluid temperature increased from 2 °C to 25 °C, the duration of the annual stabilized exploitation stage extended from 23 to 26 years. Similarly, increasing the injected circulating fluid mass flow rate from 2.78 kg/s to 16.67 kg/s prolonged the maintenance period in the annual stable mining stage from 22 to 28 years. The study further indicated that the effective thermal influence distance for each layer of thermal storage was significantly impacted by varying injection circulating fluid temperatures. These results offered theoretical insights into the heat transfer performance of medium-depth coaxial casing geothermal systems under both short- and long-term operational conditions.