The thermal performance of borehole ground heat exchangers is of significance to the efficacy of the ground source heat supply systems. This paper presents a new composite analytical model to evaluate the thermal performance of borehole ground heat exchangers within stratified ground. The model integrates critical factors influencing heat transfer, encompassing ground stratification, thermal interactions among boreholes, variability of heat flux along borehole depth, and flexible layouts of boreholes. It enables efficient computation of thermal data pertinent to heat transfer both inside and outside the boreholes during operation. Implemented in the TRNSYS platform, the model offers versatile applicability to ground-source heat pump systems, borehole thermal energy storage, and district heating and cooling networks. Model validations were carried out through four distinct experiments, covering varied borehole quantities and ground conditions, to substantiate its accuracy. Employing this model, a case study further investigated the thermal performance of a borehole field with 16 boreholes in a three-layer ground (comprising backfill soil, clay, and fine sand) extending to a depth of 63 m. Over a 60-day warm water injection period at 30 °C, the effects of borehole layout and ground stratification on the thermal performance of individual and collective boreholes were analysed. Key findings in this analysis include: (1) Across the square, L-shape, and linear layouts, the impact of layout on the thermal performance of borehole fields diminishes as the spacing increases from 1 m, 2 m, and 3 m, becoming negligible at 4-m spacing, and the positions of the most and least affected boreholes by thermal interferences vary by layout; (2) Designing a GSHP system in stratified ground using a homogenous ground model with equivalent thermal properties would overestimate the heat injection performance of the borehole field and lead to undersizing of the borehole ground heat exchangers; and (3) ground stratification should be considered when estimating the thermal performance of a borehole field, particularly when the boreholes are sparsely arranged, e.g., with spacing of 3 m or more.