It is important for clinicians to determine the risk of worsening trajectories in SSc patients. The Scleroderma Clinical Trials Consortium (SCTC) Damage Index (DI) has been developed to quantify organ damage and shows good capability for mortality and morbidity prediction in patients with SSc. This retrospective study aimed to describe the SCTC-DI in Chinese SSc patients and to find features predicting worse organ damage trajectories based on SCTC-DI. A total of 433 SSc patients who met the inclusion criteria in the Peking University Third Hospital (PKUTH-SSc) and People’s Hospital SSc cohort (PKUPH-SSc) were recruited for our study. Organ damage was relatively mild in our Chinese SSc cohort compared to other cohorts, with a mean SCTC-DI of 5.21 ± 4.60. We used both SCTC-DI ≥ 6 and ≥4 to define the high burden of organ damage and established two risk models by the LASSO algorithm, which revealed good identification of high organ damage burden (AUC = 0.689, 95% CI 0.636 to 0.742, p < 0.001 in SCTC-DI ≥ 6 model; AUC = 0.694, 95% CI 0.641 to 0.746, p < 0.001 in modified SCTC-DI ≥ 4 model). The anemia index at the baseline was included in these two models and was also independently related to organ damage progression (HR = 1.75, 95% CI 1.16 to 2.66, p = 0.008). In addition, the presence of an anti-Scl-70 autoantibody was also a predictor of progression (HR = 1.91, 95% CI 1.22 to 2.99, p = 0.005). In conclusion, anemia at the baseline was an important indicator for worse organ damage trajectories in SSc patients. We recommend using hemoglobin as a potential biomarker to evaluate organ damage in SSc patients.