With technology node scaling down to 5 nm, the narrow device geometry confines the material thermal conductivity and further aggravates the self-heating effect in gate-all-around (GAA) transistors. In this paper, we investigate the self-heating of horizontally stacked three-layer GAA nanosheet transistors by 3-D finite-element modeling (FEM) simulation. The anisotropic thermal conductivity of nanosheets with the dependence of silicon thickness and temperature is implemented in the FEM simulator to evaluate thermal behavior accurately. The impact of layout design on thermal properties is investigated comprehensively from single device to device arrays with implication on electrical performance. The results indicate that the width of nanosheet is the key parameter to make the tradeoffs between self-heating and electrical characteristic. Meanwhile, the optimizations of layout design are given to suppress the thermal effects, including self-heating, nonuniformity of temperature, and thermal crosstalk at device level. This paper will provide guidelines for layout design, thermal management, device performance, and thermal-aware reliability prediction in the GAA-stacked structure.