While universal discrete element code (UDEC) is widely used for understanding the mechanism of large-scale strata movement and the effects of mining subsidence on the environment, the fundamental knowledge of how to set vertical joint spacing (VJS) in UDEC is still not fully understood. To address the knowledge gap, we first present a novel VJS calculation method, then conduct UDEC experiments, and finally compare the predictions of UDEC models with field subsidence observation. The results suggest the following: (1) when compared to the conventional VJS setting (1× to 3× bed thickness), the maximum surface subsidence (MSS) prediction via UDEC models based on our proposed VJS setting method is closer to field observation; (2) a smaller but varying VJS setting can also have the effect of a larger VJS setting; and (3) with the increase in VJS, MSS first drops, then rises, and reaches the minimum when VJS is set at approximately 7× bed thickness. This paper provides an explanation of the VJS setting in UDEC and establishes a bridge between the KS theory and VJS, which is helpful for the sustainable development of such an UDEC modeling strategy and for a better understanding of the influences of mining subsidence on the environment in mining-affected areas.