While exercise capacity in systemic sclerosis with interstitial lung disease could be improved by exercise training, the training outcome of exercise-induced oxygen desaturation has not been examined. The aim of this study was to investigate the effect of pulmonary rehabilitation on exercise-induced oxygen desaturation during the six-minute walk test and to detect the factors affecting outcome retrospectively. Patients showing impaired exercise capacity (≤80% of predicted) and/or exercise-induced oxygen desaturation (≤-4% in SpO₂) at the end of the six-minute walk test underwent routine walking exercise. Sixteen patients with stable systemic sclerosis completed exercise training for 55 days on average. The mean six-minute walk distance improved from 467 m to 502 m (P = 0.0012). The improvement in distance was negatively related to baseline distance (R² = 0.28, P = 0.037), but was not related to parameters from pulmonary function tests and echocardiograms. Oxygen saturation was normal at rest, but was decreased in fifteen patients at the end of the test. Exercise-induced oxygen desaturation was positively related to the diffusion capacity of the lungs for carbon monoxide at baseline (R² = 0.33, P = 0.026); however, it was not related to any cardiopulmonary parameters after intervention. Seven of sixteen patients ameliorated exercise-induced oxygen desaturation or showed no oxygen desaturation after exercise training, while others deteriorated. No cardiopulmonary parameters affected the training outcome of exercise-induced oxygen desaturation. Exercise train ing was beneficial in improving exercise tolerance, but training effects and mechanisms on exercise-induced oxygen desaturation still need more studies to be explained.