Sarcopenia is a potential risk factor for adverse outcomes in haematopoietic cell transplantation (HSCT) recipients. We aimed to explore longitudinal body changesin muscle and adipose mass and their prognostic value in allogeneic HSCT-treated severe aplastic anaemia (SAA) patients. We retrospectively analysed consecutive SAA patients who underwent allogeneic HSCT between January 2017 and March 2022. Measurements of pectoral muscle and corresponding subcutaneous fat mass were obtained via chest computed tomography at baseline and at 1month, 3months, 6months, and 12months following HSCT. Sarcopenia was defined as pectoral muscle index (PMI) lower than the sex-specific median at baseline. Changes in body composition over time were evaluated by generalized estimating equations. Cox regression models were used to investigate prognostic factors affecting overall survival (OS) and failure-free survival (FFS). A nomogram was constructed from the Cox regression model for OS. We included 298 adult SAA patients (including 129 females and 169 males) with a median age of 31years [interquartile range (IQR), 24-39years] at baseline. Sarcopenia was present in 148 (148/298, 50%) patients at baseline, 218 (218/285, 76%) patients post-1month, 209 (209/262, 80%) patients post-3month, 169 (169/218, 78%) patients post-6month, and 129 (129/181, 71%) patients post-12month. A significant decrease in pectoral muscle mass was observed in SAA patients from the time of transplant to 1year after HSCT, and the greatest reduction occurred in post 1-3months (P<0.001). The sarcopenia group exhibited significantly lower 5-year OS (90.6% vs. 100%, log-rank P=0.039) and 5-year FFS (89.2% vs. 100%, log-rank P=0.021) than the nonsarcopenia group at baseline. Sarcopenia at baseline (hazard ratio, HR, 6.344; 95% confidence interval, CI: 1.570-25.538; P=0.01; and HR, 3.275; 95% CI: 1.159-9.252; P=0.025, respectively) and the delta value of the PMI at 6months post-transplantation (ΔPMI6) (HR, 0.531; 95% CI: 0.374-0.756; P<0.001; and HR, 0.666; 95% CI: 0.505-0.879; P=0.004, respectively) were demonstrated to be independent prognostic factors for OS and FFS in SAA patients undergoing HSCT, and were used to construct the nomogram. The C-index of the nomogram was 0.75, and the calibration plot showed good agreement between the predictions made by the nomogram and actual observations. Sarcopenia persists in SAA patients from the time of transplant to the 1-year follow-up after HSCT. Both sarcopenia at baseline and at 6months following HSCT are associated with poor clinical outcomes, especially in patients with persistent muscle mass loss up to 6months after transplantation.