Children and adolescents with autism spectrum disorder (ASD) frequently present with mental health comorbidities and behavioral crises, necessitating inpatient care. However, evidence-based guidelines for psychotropic medication use in specialized inpatient settings remain limited, particularly in non-Western contexts. This study examined the clinical characteristics and prescribing patterns among 269 hospitalized ASD patients (2012–2023), with a focus on how intellectual disability (ID) influences medication decisions. A retrospective analysis was conducted using electronic medical records to assess mental disorders, behavioral challenges, and psychotropic medication use at discharge. Logistic regression analyses was performed to examine factors associated with medication prescribing patterns, including the impact of ID status. Psychotropic medication use was highly prevalent (96.7%), with antipsychotics (89.96%) being the most frequently prescribed class, followed by anxiolytics (35.32%) and antidepressants (33.09%). ID was significantly associated with distinct prescribing patterns: patients with ID had 63% lower odds of antidepressant use (aOR = 0.37, p = 0.001) and 80% lower odds of ADHD medication use (aOR = 0.20, p = 0.009), while being more likely to receive antipsychotics (aOR = 2.74, p = 0.049) and experience polypharmacy (aOR = 1.89, p = 0.028). Additionally, disruptive behaviors and age were key predictors of antipsychotic use, whereas suicidal thoughts/attempts or SIBs independently predicted antidepressant prescribing. These findings suggest that ID status plays a critical role in shaping psychotropic prescribing practices beyond symptom severity alone, potentially reflecting diagnostic overshadowing and safety concerns. Future research should focus on developing tailored clinical assessment tools and treatment protocols for ASD populations with and without ID, while enhancing individualized medication monitoring to optimize therapeutic outcomes.