Sodium and potassium ions batteries (SIBs, PIBs) as the ideal substitutes for lithium ion batteries (LIBs) applied in large-scale energy storage have attracted wide concerns due to the same work principle of LIBs, rich abundance, and low-cost features. However, the key challenge in the Na+/K+ storage field is the shortage of suitable anode materials because the common anode for LIBs, graphite, cannot effectively accommodate Na+ and K+. Molybdenum chalcogenides as anode materials for SIBs/PIBs have triggered great attention due to their special electronic/crystal structures and high specific capacities. However, their huge volumetric fluctuation upon repeated cycles will lead to serious capacity loss, and the low electrical conductivity will restrict the rate capability. In this review, the latest progress for various molybdenum chalcogenides in SIBs/PIBs including electrode structure design, reaction mechanism, and electrolyte optimization have been summarized in detail for performance promotion. Meanwhile, the existing challenges and future perspectives are proposed to provide favorable guidance for their further applications as next-generation rechargeable batteries.