Advanced battery electrodes require a cautious design of microscale particles with built-in nanoscale features to exploit the advantages of both micro- and nano-particles relative to their performance attributes. Herein, the dynamic behavior of nanosized Sn clusters and their host pores in carbon nanofiber) during sodiation and desodiation is revealed using a state-of-the-art 3D electron microscopic reconstruction technique. For the first time, the anomalous expansion of Sn clusters after desodiation is observed owing to the aggregation of clusters/single atoms. Pore connectivity is retained despite the anomalous expansion, suggesting inhibition of solid electrolyte interface formation in the sub-2-nm pores. Taking advantage of the built-in nanoconfinement feature, the CNF film with nanometer-sized interconnected pores hosting Sn clusters (approximate to 2 nm) enables high utilization (95% at a high rate of 1 A g-1) of Sn active sites while maintaining an improved initial Coulombic efficiency of 87%. The findings provide insights into electrochemical reactions in a confined space and a guiding principle in electrode design for battery applications.|The dynamic behavior of nanosized Sn clusters and their host pores in carbon nanofibers during sodiation and desodiation is revealed. The deep learning-assisted 3D electron microscopic reconstruction technique of CNFs reveals the anomalous expansion of Sn clusters even after desodiation and the remaining pore connectivity despite cluster expansion and solid electrolyte interface formation.image