Radiation-induced bone injury (RIBI) is a delayed complication of radiotherapy that causes progressive bone loss and impairs skeletal integrity. In this study, we investigated whether phenylethanoid glycosides (PGs) from Cistanche tubulosa (Schenk) Wight could improve RIBI and explored the underlying mechanism. Using a mouse model of delayed radiation-induced bone injury, we found that PGs improved body weight recovery, grip strength, and oxidative stress status after irradiation. Through micro-computed tomography and histological staining to evaluate bone microstructure, it was found that PGs could reduce osteoclast activity after radiation and restore trabecular microstructure, thereby alleviating bone loss caused by radiation. Single-cell RNA sequencing of femoral bone marrow revealed that radiation disrupted the cellular composition of the bone marrow microenvironment and impaired osteogenic programs in bone marrow mesenchymal stem cells. PGs partially restored osteogenic differentiation-related signatures and suppressed adipogenic bias. In osteoblasts, we identified Gremlin-1 (Grem1), a negative regulator of BMP signaling, as a key radiation-responsive gene that was markedly upregulated after irradiation and downregulated by PGs. Western blotting in femoral tissue and MC3T3-E1 cells confirmed that PGs suppressed radiation-induced Grem1 expression. In vitro, PGs promoted alkaline phosphatase activity and mineralization in irradiated osteoblasts. These findings suggest that PGs mitigate RIBI by attenuating oxidative stress, improving bone remodeling, restoring the bone marrow microenvironment, and relieving Grem1-mediated inhibition of osteogenesis. Grem1 may represent a potential therapeutic target for radiation-associated skeletal injury.