Sodium ion batteries (SIBs) have been considered as a promising candidate to supersede lithium ion batteries, however, the lack of suitable electrode materials for efficient Na-storage still hinders its practical use. Hence, this work reports a general and effective way to in-situ construction of heterostructured SnSe/SnTe nanodots encapsulated in nitrogen-doped mesoporous carbon matrix (SnSe/SnTe@N-CNFs). In such unique architecture, the porous N-CNFs matrix cannot only provide high electronic/ion conductivity but also alleviate the volume change of SnSe and SnTe, leading to rapid kinetics and robust structure, whereas the ultrasmall SnSe/SnTe heterostructure with built-in interfacial driving force can promote charge transfer kinetics. Meanwhile, the abundant defective sites induced from high-level N-doping is beneficial to Na+ storage. Besides, the formed Sn–C, Se–C, and Te–C bonds can improve the interfacial interaction between SnSe/SnTe and N-CNFs, thus enhancing electronic conductivity, suppressing the aggregation and detachment of active components, and ensuring rapid kinetics and structural integrity. When evaluated as an anode for SIBs, the as-prepared SnSe/SnTe@N-CNFs exhibits high reversible capacity, remarkable cycling stability, and superior rate capability. This work can offer an efficient and universal strategy for designing advanced anode materials with exceptional performance.