Prolonged bedtime smartphone use is often associated with poor sleep quality and daytime dysfunction. In addition, the unstructured nature of smartphones may lead to excessive and uncontrolled use, which can be a cardinal feature of problematic smartphone use. This study was designed to investigate functional connectivity of insula, which is implicated in salience processing, interoceptive processing, and cognitive control, in association with prolonged bedtime smartphone use. We examined resting-state functional connectivity (rsFC) of insula in 90 adults who used smartphones by functional magnetic resonance imaging (fMRI). Smartphone time in bed was measured by self-report. Prolonged bedtime smartphone use was associated with higher smartphone addiction proneness scale (SAPS) scores, but not with sleep quality. The strength of the rsFC between the left insula and right putamen, and between the right insula and left superior frontal, middle temporal, fusiform, inferior orbitofrontal gyrus and right superior temporal gyrus was positively correlated with smartphone time in bed. The findings imply that prolonged bedtime smartphone use can be an important behavioral measure of problematic smartphone use and altered insula-centered functional connectivity may be associated with it.