Spinal cord injury (SCI) can disrupt neural connections and impair locomotion and sensation function. Currently, biomaterials containing neural progenitor cells (NPCs) are widely used to replace damaged tissue or provide support for neural regeneration following SCI. Immunosuppressive drugs (ISDs) are commonly utilized to ensure the survival of transplanted NPC in SCI. However, the potential benefits and risks of using ISDs in NPC transplantation with biomaterials for SCI repair has not been deeply studied. Herein, an orderly aligned collagen sponge scaffold (ACSS) combined with human embryonic spinal cord neural progenitor cells (hscNPCs) was transplanted into SCI rats, with or without ISDs. Results showed that ISDs suppressed cell -mediated immune and inflammatory responses, maintained early survival and differentiation capacity of transplanted cells, and promoted early functional recovery of SCI rats. However, ISDs did not influence endogenous nerve regeneration, angiogenesis, glial scarring or long-term functional recovery after ACSS and hscNPC transplantation. Additionally, ISDs can induce toxicity in multiple organ and impact the survival of animals after SCI. Thus, careful evaluation of the benefits and risks is necessary to maximize therapeutic efficiency when administrating ISD in combination with scaffold -loaded NPCs for SCI repair.