Real-temperature topological magnetic dynamics in functional materials is governed by coupled lattice and spin evolution, yet remains inaccessible to predictive simulation at device-relevant scales. As a flagship example, thermally driven helix-to-skyrmion transformation in FeGe requires atomistic resolution, explicit lattice motion, and micrometer-scale domains to resolve device-scale topological texture formation. We combine a spin-constrained density-functional-theory-trained neuro-evolution potential with a structure-preserving spin-lattice integrator within one machine-learned framework. Architecture-specific optimizations, kernel fusion, SVE2 vectorization, and NUMA-aware data layout deliver a seven orders-of-magnitude speedup over prior spin-aware methods. Deployed on LineShine exascale supercomputer, the full application scales to 12.45 million CPU cores with 89.7% weak-scaling efficiency, enabling simulations of 1.34 trillion atoms and an equal number of spins while reaching 48.5 PFLOPS in double precision. The simulations directly resolve real-temperature skyrmion nucleation and reorganization at previously inaccessible scales, establishing a new regime for predictive simulation of coupled spin-lattice topological magnetic dynamics.