Nanostructured silicon with its high theoretical capacity and ability to accommodate volume expansion has attracted great attention as a promising anode material for Lithium ion (Li-ion) batteries. Liquid metal dealloying method, is a novel method to create nanoporous silicon (np-Si). The assembled Li-ion batteries based on such np-Si anode can be cycled beyond 1500 cycles, in 1000 mA h/g constant capacity cycling mode with consistent performance; however, it suffers from degradation after ~ 460 cycles, while being cycled under 2000 mA h/g. To reveal the failure mechanism and differences in the morphological evolution in different capacity cycling modes in the np-Si anode, we conducted synchrotron X-ray nano-tomography studies. The three dimensional (3D) morphological evolution was visualized and quantified as a function of the number of cycles and cycling capacities. By comparing the 3D morphology under each cycling condition and correlating these 3D morphological changes with cycling-life performance, we elucidate the failure mechanism of the np-Si electrodes resulting from a mesoscopic to macroscopic deformation, involving volume expansion and gradual delamination. In particular, the shorter cycling life in higher-capacity cycling mode stems from particle agglomeration. Overall, while the nanoporous structure can accommodate the volume expansion locally, these mesoscopic and macroscopic deformations ultimately result in heterogeneous stress distribution with faster delamination. The work thus sheds the light on the importance to consider the structural evolution at the mesoscopic and macroscopic scales, while designing nano-structured energy storage materials for enhanced performances, particularly for long cycling-life durability.