Estonian is a quantity language where both a primary duration cue and a secondary pitch cue exist, whereas Chinese is a tonal language that features a dominant use of pitch. Native speakers of both languages (63 Estonian and 61 Chinese participants) participated in a mismatch negativity (MMN) experiment where stimuli in both languages and their non-linguistic equivalents (i.e., pure tones) were discriminated in terms of duration change, pitch change, and duration plus pitch change. The MMN experiment was followed by a behavioral discrimination experiment where non-native stimuli were presented. Chinese participants showed right lateralized MMNs and, behaviorally, a low discrimination accuracy to the duration change in the Estonian stimuli and their non-linguistic equivalents, suggesting that they perceived duration as acoustic information without linguistic meaning. While no group difference was found in perceiving the pitch change in the Estonian stimuli, Chinese participants showed larger MMNs and a higher accuracy than Estonian participants to the pitch change in the Chinese stimuli, suggesting a relatively better pitch discrimination ability than Estonian participants. Estonian participants showed larger MMNs than Chinese participants to the pure tones that resembled the Estonian stimuli containing both duration and pitch changes, suggesting that linguistically-relevant cues can influence the processing of non-linguistic stimuli. Our results indicate that long-term familiarity with specific sound features in one’s native language affects the perception of duration and pitch and that such an effect is not specific to the language domain.