Large-scale water pit thermal energy storage (PTES) promotes solar district heating (SDH) system as one of the most potential renewable applications for carbon neutrality. PTES needs vast investment and operates in a complicated system with numerous components, highlighting the need for a suitable simulation tool for tech-economic and feasibility investigations. This paper experimentally and theoretically investigated the long-term thermal performance of a 60,000 m3 PTES in Dronninglund, Denmark. Five years measurements were analyzed to investigate the development of temperatures, heat flows, and thermal stratification in heat storage. A modified 2D model was proposed to calculate the thermal performance of the large-scale PTES based on the XST model in TRNSYS. The results showed that the developed model predicts well the storage temperatures and the heat flows. For one-year validation, the deviations of annual charged/discharged energy, internal energy content, and annual thermal loss between the model and the measurements were 2.0%/1.8%, 2.8% and 1.3%, respectively. The Dronninglund PTES showed 90.1% storage efficiency in the five-year investigation due to its high storage utilization cycle of 2.16. Even without any insulation on the sidewall and the bottom of the PTES, the average thermal loss from the two parts only accounted for 32.3% of total heat loss. Meanwhile, the soil region needed four years to stabilize. Approx. 24.4% of the heat loss in summer from the sidewall and the bottom is regained by the PTES in winter, when there is a low temperature in the heat storage. The findings of the paper serve as a good reference for designers and practitioners of water pit heat storage.