Auditory hyper-reactivity is a common sensory-perceptual abnormality in autism spectrum disorders (ASD), which interrupts behavioral adaptation. We investigated acoustic startle response (ASR) modulations in 17 children with ASD and 27 with typical development (TD). Compared to TD, children with ASD had larger ASR magnitude to weak stimuli and more prolonged peak startle-latency. We could not find significant difference of prepulse inhibition (PPI) or habituation in ASD children compared to TD. However, habituation and PPI at 70-dB prepulses were negatively related to several subscales of Social Responsiveness Scale and the Strengths and Difficulties Questionnaire, when considering all children. Comprehensive investigation of ASR and its modulation might increase understanding of the neurophysiological impairments underlying ASD and other mental health problems in children.