Background: Substance abuse among young people has become a serious public health problem for years. The risk of relapse among illicit drug use is essential for developing adequate substance reuse prevention policies. The purpose of the current study is to investigate the potential predictor in long-term relapse rates among young patients that underwent a family-based treatment program. Methods: To perform this study, 103 young patients with substance use (mean age: 16.2 years, 78.6% male) were referred to participate in a 10-week family-based treatment program. At the beginning and at the end of the treatment, the patients were required to fill out the Chinese Craving Beliefs Questionnaire (CCBQ), the Adolescents' Behavior-problem Scale (ABS), and the Family APGAR. Furthermore, the patients' caregivers had to fill out the Family APGAR, the 12-item version of the Chinese Health Questionnaire (CHQ), and the Parenting Stress Index (PSI). All patients were followed up for 5 years in order to observe their long-term outcomes regarding substance use relapse. Results: During the 10-week family-oriented programs, the CCBQ scores, the CHQ scores and the Child-domain of PSI significantly decreased. Better changes in patients' behavioral problems during the treatment program predicted a lesser likelihood of substance use relapse in the subsequent 5 years. Furthermore, methamphetamine or 3,4-methylenedioxy-methamphetamine use and living in single-parent families were two factors associated with higher relapse rates. Conclusions: The changes in patients' behavioral problems during the treatment program may serve as a predictor of substance use relapse over the subsequent 5 years. This study's findings provide insight about substance use prevention and serve as a reference for policy-making.