The optimal use of geothermal energy necessitates the performance evaluation and economic analysis of the geothermal heating systems. This work presented a field study of the long-term operating performance of a geothermal heating system in Xixian New Area, China. Nine deep coaxial ground heat exchangers (GHEs) with depths of 2,500 m were adopted for space heating to the residential buildings, with a total heating area and heating load of 136,097.71 m2 and 6,082 kW, respectively. The system’s 30-year running performance at various volumetric flow rates and operating modes was simulated. Through response surface analysis and multi-objective optimization, the levelized cost of energy (LCOE) and payback period were obtained based on the thermal performance analysis. It is concluded that the operating parameters have a significant impact on the system economy. When the daily operating time reduces from 24 hours to 8 hours, the payback period will be lowered from more than 25 years to approximately 11 years. When the volumetric flow rate is 35 m3·h-1, the examined system achieves the lowest LCOE. The minimum values of LCOE are 13.2 $/GJ, 11.6 $/GJ, 9.4 $/GJ, 7.8 $/GJ and 5.6 $/GJ when the system operates 24 hours (continuous operation), 20 hours, 16 hours, 12 hours and 8 hours a day, respectively. With the optimal flow rate, the average heat exchange rate of the single GHE increases from 295 kW to 519 kW after 30 years of operation when the daily operating time is reduced from 20 hours to 8 hours. The proposed method and findings can be used to guide the high-efficiency operation, which is conducive to reducing operating costs of geothermal heating systems.