Red phosphorus has been recognized as a promising anode material for sodium ion batteries (SIBs) because of its large theoretical capacity and suitable sodiation potential. However, low conductivity, large volume change, and incomplete alloy/de-alloy caused by a high formation energy (Ef) of a Na3P sodiation product hinder its practical applications. Herein, we found that element Se can offer a relatively low Ef for a sodiation product and form a robust P–Se bond, which effectively improves the conductivity and Na+ reaction kinetics. In this direction, heteroatomic amorphous phosphorus-rich phosphorus selenides molecules encapsulated into porous carbon nanotubes (a-P9Se@pCNTs) were successfully prepared, showing a highly reversible Na+ storage ability with high initial Coulombic efficiency of 85.9%, a high specific capacity of 2215 mAh/g, and an excellent rate capability even at a high mass loading of ∼70 wt %. The combined density functional theory calculations and comprehensive experimental study authenticate that the lower formation energy of a sodiated product and the fast ion transport ability of P9Se can significantly accelerate reversible alloy/de-alloy reaction, improve pulverization issues, and restrain the undesired decomposition of an electrolyte, resulting in full nearly utilization of an active material and a stable solid electrolyte interphase. The present finding demonstrates an innovative design pathway for a red phosphorus anode and guides substantial progress of energy storage devices.