Background: Young children with special needs greatly rely on their parents to support their daily living activities; parental compliance may have great impact on the implementation of health promotion activities among those children. This study aimed to investigate the parental compliance towards oral health education (OHE) among children with special healthcare needs (SHCN). Method: The participants were 306 parents whose children had participated in a 24-month OHE program for preschool children with SHCN. The primary outcome of this cross-sectional study was parental compliance towards the OHE program. Parents’ oral health literacy (OHL) was assessed by a validated tool. Parents’ socioeconomic status, attitudes towards OHE topics, perceptions of children’s oral hygiene status, and usefulness of OHE materials were collected via questionnaires. Results: A higher dropout rate was observed among parents who perceived that their children had unfavorable oral hygiene status (p = 0.038), or parents who had poor OHL skills (p = 0.015). Parental noncompliance was more likely to be observed among parents who perceived that the OHE materials were not useful for their children (OR = 3.63, 95% CI 1.56 to 8.47, p = 0.003), or parents whose children had been diagnosed with developmental delays (OR = 5.45, 95% CI 1.59 to18.74, p = 0.007). Conclusion: Non-compliance existed among parents whose children had received OHE intervention. Parental compliance towards OHE intervention might be associated with parents’ OHL skills, usefulness of OHE materials, and children’s developmental conditions. OHE programs should be individually tailored to support children whose parents are at a higher risk of noncompliant behaviors.