This paper reports unique highly porous carbon-coated Si nanoparticles with canyon-like surfaces (cpSi@C) prepared by pseudomorphic transformation of wrinkled silica nanoparticles (WSNs) via magnesiothermic reduction and subsequent pyrolytic deposition of carbon. The pseudomorphic transformation of soft-template-based WSNs with large pore dimensions provides Si nanoparticles with additional porosity owing to their unique canyon-like surface structure. This degree of porosity is not achievable using conventional soft-template-derived porous SiO₂ materials owing to their smaller pore dimensions. The free volume space in the cpSi@C particles is 419% of their Si volume, which is sufficient to fully accommodate Si volume expansion during cycling. Furthermore, the conformal carbon coating allows cpSi@C to enhance its electrical conductivity. cpSi@C exhibits a high specific charge capacity of 822 mA h g⁻¹ after 200 cycles at a current density of 0.5 A g⁻¹, which is 59.1% of the initial charge capacity. A comparative study with respect to other porous Si-based materials clearly revealed that the unique canyon-like structure synthesized in this study, with its additional pore volume and smaller Si dimensions, exhibits enhanced electrochemical performance.