This study aimed to develop and empirically validate a multicomponent model explaining harmful sexual behaviour (HSB) in individuals with autism spectrum disorder (ASD) and comorbid intellectual disability (ID), integrating neurodevelopmental, psychological, social, environmental, and systemic factors. A mixed-method model-development design was implemented across three phases: systematic literature synthesis, empirical component mapping, and expert validation using a modified Delphi approach. A sample of 124 individuals with ASD and ID was assessed using standardized measures of cognitive functioning, adaptive behaviour, emotional regulation, trauma exposure, and social cognition. Structural equation modeling (SEM) and hierarchical regression were applied to test direct and indirect relationships that lead to the severity of HSB. Emotional dysregulation became a factor which has the most significant predictor of the severity of HSB (r = 0.63, p < 0.001; β = 0.47, p < 0.001). The regression model was able to explain 54% of the variance (Adjusted R2 = 0.54), where the SEM explained 62% with a satisfactory model fit (CFI = 0.93; RMSEA =0.067). Neurodevelopmental vulnerability exerted both direct and indirect effects through social cognition deficits, and trauma exposure significantly moderated behavioural expression (β = 0.29, p < 0.05). Harmful sexual behaviour in ASD with ID is best understood through a dynamic, interaction-based framework. Targeting emotional regulation, trauma-informed care, and social cognition may enhance prevention and intervention strategies.