Sodium-ion batteries (SIBs) are promising power sources due to the low cost and abundance of battery-grade sodium resources, while practical SIBs suffer from intrinsically sluggish diffusion kinetics and severe volume changes of electrode materials. Metal-organic framework (MOFs) derived carbonaceous metal compound offer promising applications in electrode materials due to their tailorable composition, nanostructure, chemical and physical properties. Here, we fabricated hierarchical MOF-derived carbonaceous nickel selenides with bi-phase composition for enhanced sodium storage capability. As MOF formation time increases, the pyrolyzed and selenized products gradually transform from a single-phase Ni₃Se₄ into bi-phase NiSe_x then single-phase NiSe₂, with concomitant morphological evolution from solid spheres into hierarchical urchin-like yolk-shell structures. As SIBs anodes, bi-phase NiSe_x@C/CNT-10h (10 h of hydrothermal synthesis time) exhibits a high specific capacity of 387.1 mAh/g at 0.1 A/g, long cycling stability of 306.3 mAh/g at a moderately high current density of 1 A/g after 2,000 cycles. Computational simulation further proves the lattice mismatch at the phase boundary facilitates more interstitial space for sodium storage. Our understanding of the phase boundary engineering of transformed MOFs and their morphological evolution is conducive to fabricate novel composites/hybrids for applications in batteries, catalysis, sensors, and environmental remediation.