Thermal management is one of the major challenges facing the development of three-dimensional (3D) chip stacks. Recently, experimental studies have shown that neck-based thermal structure (NTS) between chip layers formed by drying of colloidal suspension in cavity filled with micro-size particles can improve the vertical heat conduction threefold. However, a deep understanding of the mechanisms of neck formation and its influence on heat conduction is still lacking. In this paper, we numerically study the effects of three parameters, i.e., initial nanoparticle concentration, drying temperature and chip surface wettability on neck formation between filler particles and on the resulting heat conduction of the NTS. With increasing nanoparticle concentration, the size and number of necks increase, resulting in an increased effective thermal conductivity (ETC) of NTS. The drying temperature is found to have only little influence on the ETC of resultant NTS, while the neck size and spatial distribution become more uniform at higher drying temperature. When reducing the wettability of the top and bottom surfaces of the cavity, the necks shrink in size until completing evacuating at the top and bottom layers, while the size of the necks between filler particles in the middle height of the cavity expands slowly. In consequence, the ETC of NTS drops at an increasing rate. Being able to reveal the underlying multiple mechanisms of two-phase flow, phase change and heat transport, the current numerical study suggests optimal values for the deposition process, with initial nanoparticle concentration over 0.8%, a drying temperature of 60°C and a uniform contact angle of 30° for practical production of NTS.