<p>It has been widely recognized that moral decisions are processed by both emotional and reasoning systems. But the mechanisms for difficulty perceptions and how are they related to the two systems is still unclear. Here, we tested 3 potential factors, value difference, mean value of the options, and values of the victims. A new paradigm was developed to quantify the option values and to dissociate emotional and utilitarian values. Hypothesis were tested with the correlations of perceived difficulties and those 3 factors with linear mixed-effect model. First, data showed that both emotional and utilitarian value differences are negatively correlated with perceived difficulties, demonstrating its fundamental role in difficulty perception. Then, it was found that higher mean emotional value of the options adds difficulty to reasoning-motivated decisions, while higher mean utilitarian value of options showed no effect, indicating that the interaction can be asymmetric between the two systems. Lastly, both emotional and utilitarian values of the victim (i.e. unchosen) are positively correlated with perceived difficulties, showing that victim is also a critical factor. These results update the framework of difficulty perception in moral decisions, adding more to the basic value difference.</p>