The pulvinar is important in selective attention, particularly to visual stimuli under the focus of attention. However, the pulvinar is assumed to process emotional stimuli even outside the focus of attention, because of its tight connection with the amygdala. We therefore investigated how unattended emotional stimuli affect the pulvinar and its effective connectivity (EC) while considering individual differences in selective attention. fMRI in 41 healthy human subjects revealed that the amygdala, but not the pulvinar, more strongly responded to unattended fearful faces than to unattended neutral faces (UF > UN), although we observed greater EC from the pulvinar to the amygdala. Interestingly, individuals with biased attention toward threat (i.e., attentional bias) showed significantly increased activity (UF > UN) and reduced grey matter volume in the pulvinar. These individuals also exhibited stronger EC from the pulvinar to the attention-related frontoparietal network (FPN), whereas individuals with greater attentional control showed more enhanced EC from the pulvinar to the amygdala, but not the FPN (UF > UN). The pulvinar may filter unattended emotional stimuli whose sensitivity depends on individual threat-related attentional bias. The connectivity patterns of the pulvinar may thus be determined based on individual differences in threat-related attentional bias and attentional control.