For the issue of excessive mass in the chain drive system of long-distance scraper conveyors, this paper proposes a method to optimize the scraper chains by integrating discrete element simulation (DEM) with topological optimization. The aim is to reduce the system’s mass while maintaining its transportation capacity and structural integrity. The SGZ1000 model scraper conveyor with a length of 400 m was selected as the research object. Studies have demonstrated that for 56 × 187 mm scraper chains, a non-equally spaced configuration (6p-8p-6p, where p represents the chain link pitch) outperforms an equally spaced configuration (6p). While ensuring the conveying capacity of the scraper chains, the optimized configuration reduces the number of scrapers in chains of equal length by 11.11%. For a 400 m scraper conveyor, adopting the 6p-8p-6p scraper spacing reduces the number of scrapers by 72 and decreases the mass by 6357.6 kg. Additionally, utilizing topologically optimized scrapers further reduces the total mass by 10,131.4 kg. Compared to the original chain drive system, the optimized scraper chains have reduced the mass by 26.2%, significantly lowering the no-load energy consumption of the long-distance scraper conveyor.