Music surrounds us, and there is no denying that music in visual media can shape and evoke emotions. Yet, understanding how musical preference influences emotions through audio and visual stimuli remains an important task. To address this task, we investigated the role of musical preference effect on perceived emotions induced through music and visual stimuli (i.e., animation), using a 7-point scale for valence-arousal ratings and physiological responses in electroencephalogram (EEG) band power. The perceived emotions are categorized into four states: happiness, calmness, fear, and sadness. One emotional state contains 4 sessions: (1) Preferred Music, (2) Unfamiliar Music, (3) Preferred Music+Animation, and (4) Unfamiliar Music+ Animation. Behavior-wise, the rating results showed that the presence of preferred music resulted in higher perceived valence ratings, particularly in happiness. However, no stimulus had a significant effect on perceived arousal ratings and satisfaction ratings. Physiologically, the EEG indexes showed that the presence of preferred music appears to affect an increase in alpha power across various emotions except sadness, whereas unfamiliar music seems to affect beta power, particularly in happiness and calmness. Overall, these findings supported that musical preference is an affective factor reflecting the levels of valence and alpha power in EEG. Nevertheless, our findings did not confirm a significant difference between only preferred music and combining it with animation. Interestingly, we also found that participants were more likely to be attracted to and perceive positive (i.e., happiness and calmness) emotions easily through preferred music and/or visual stimuli than negative (i.e., fear) emotions.