Aim. The purpose of this study was to investigate the toothbrushing habits and risk indicators among aboriginal children with severe early childhood caries (S-ECC). Methods. This was a cross-sectional purposive sampling study that included 281 aboriginal children aged 2 to 5 years living in remote regions in southern Taiwan. Participant received dental examinations and questionnaires that were completed by caretakers. Results. From among the 281 participants, 238 children (84%) presented with S-ECC. A low-frequency toothbrushing habit among the children with S-ECC was associated with caretakers with low-frequency toothbrushing (P = .001). The odds ratio of a child using improper toothbrushing methods having a caretaker with a low brushing frequency was 3.45 (P = .0157). Conclusions. Low-frequency toothbrushing and improper toothbrushing methods were associated with S-ECC. The caretakers’ brushing frequency was a risk indicator associated with the children’s poor oral hygiene.