<p>Sarcopenia has been established as an adverse prognostic factor in severe aplastic anemia (SAA) patients treated with allogeneic hematopoietic stem cell transplantation (HSCT), which is a complex and important process of hematopoietic and immune reconstitution (IR). Our study aimed to investigate the effect of sarcopenia on the longitudinal IR dynamics in SAA patients following HSCT. We retrospectively analyzed lymphocyte subsets, including CD3⁺, CD4⁺, CD8⁺ T cells, CD19⁺ B cells and natural killer (NK) cells, in 279 SAA patients during the first year post-HSCT. Sarcopenia was diagnosed using sex-specific pectoral muscle index (PMI) thresholds calculated from baseline chest CT. Early IR for each cell subset was defined as cell counts at or above the median value at 3 months post-HSCT. The association between early IR and HSCT outcome, as well as factors influencing early IR were evaluated. The cohort (median age of 31 years, range, 24–39 years, 56.3% male) had a baseline sarcopenia prevalence of 49.8% (139/279). Compared with the non-IR group, early IR of CD3⁺, CD4⁺ and CD8⁺ T cells was associated with superior 5-year OS and FFS rates (<i>P</i> &lt; 0.05). Multivariable analysis confirmed early IR of CD8⁺ T cells as an independent OS predictor (HR = 0.193, 95% CI: 0.043–0.873; <i>P</i> = 0.033). However, baseline sarcopenia was independently associated with impaired early IR of CD8⁺ T cells (OR = 1.863, 95% CI: 1.110–3.126; <i>P</i> = 0.019). Addressing baseline sarcopenia may promote early IR of CD8⁺ T cells following HSCT in SAA patients, potentially improving posttransplant clinical outcomes.</p>