Background: Various controversial conclusions exist regarding the reproductive toxicity of cyclophosphamide, creating uncertainties about the recovery timeline of maternal reproductive capacity and offspring health. Methods: Using a mouse model with a clinically relevant cyclophosphamide dosing regimen, we examined the recovery of female reproductive function after exposure and the long-term survival and development of their offspring. Results: Our findings revealed that cyclophosphamide exposure shortened the maternal reproductive lifespan, characterized by early fertility impairment at one week (p < 0.05), transient recovery at two weeks (p > 0.05), a subsequent decline at four weeks with further deterioration, and eventual progression to infertility at six months (p < 0.01). F1 pups from the cyclophosphamide group exhibited growth restriction, higher mortality rates, delayed pubertal onset, and impaired neurodevelopment during long-term follow-up. Although some parameters transiently improved at 2 weeks post-withdrawal, these abnormalities persisted or recurred at 4 and 8 weeks, indicating that developmental defects were not lessened by prolonging the medication withdrawal period. Conclusions: These findings demonstrate irreversible gonadotoxicity and developmental toxicity following cyclophosphamide exposure in this mouse model.