The present work examines the NOx emission characteristics of a premixed micro-combustion system with a perforated plate implemented. For this, a three-dimensional (3D) computational model involving a detailed chemical-kinetic mechanism for ammonia-oxygen combustion in the micro-combustor is developed. The model is first validated with the experimental measurements available in the literature before conducting comprehensive analyses. It is found that implementing a perforated plate in the micro-combustion system creates a flow recirculation zone downstream characterized by a low flame temperature and combustion speed. Meanwhile, the conjugate heat transfer between the combustion products and the inner combustor walls is shown to play a key role in the NO generation by relocating the flame in the axial direction and thus changing the chemical reaction rate. Furthermore, the preferential diffusion caused by the variation in the mass diffusivity of different species and the two-dimensionality flow is identified to vary significantly in comparison with the case in the absence of the perforated plate, especially in the vicinity of the recirculation zone. This diffusion effect results in the considerable drop in the N/O atomic ratio, primarily due to the reduction and increase of O2 and H2O, together with less available N2, and consequently affecting the NO generation rate. This work confirms that the flow field, the conjugate heat transfer as well as the preferential diffusion effect could be regarded as the potential mechanisms leading to the NOx emission variation in the recirculation zones.