Magnetic skyrmions, despite being promising ultra‐low energy information carriers with wide bandwidth and nonvolatility, are not used for any universal scalable logic system. Here, a detailed understanding of skyrmion motion in nanowires under different geometries and drive conditions is established. Then, these insights are used to introduce a general Boolean‐universal gate block system with components, emulation, and simulation algorithms. The resulting system can collectively form a scalable, cascadable, and universal skyrmion logic system and produce arbitrary logic designs. The NOR, AND, OR, NAND, XNOR, and FULL ADDER gates are provided here as example demonstrations of the system. The toolkit lays the foundation for bridging the gap between theoretical exploration and practical implementation of skyrmion‐based computing. The skyrmion block components may help reduce energy consumption per logic operation after eliminating Joule heating. The insights and designs may help skyrmions be used in state‐of‐the‐art electronic design automation.