Semantic unification during sentence comprehension has been associated with amplitude change of the N400 in event-related potential (ERP) studies, and activation in the left inferior frontal gyrus (IFG) in functional magnetic resonance imaging (fMRI) studies. However, the specificity of this activation to semantic unification remains unknown. To more closely examine the brain processes involved in semantic unification, we employed simultaneous EEG-fMRI to time-lock the semantic unification related N400 change, and integrated trial-by-trial variation in both N400 and BOLD change beyond the condition-level BOLD change difference measured in traditional fMRI analyses. Participants read sentences in which semantic unification load was parametrically manipulated by varying cloze probability. Separately, ERP and fMRI results replicated previous findings, in that semantic unification load parametrically modulated the amplitude of N400 and cortical activation. Integrated EEG-fMRI analyses revealed a different pattern in which functional activity in the left IFG and bilateral supramarginal gyrus (SMG) was associated with N400 amplitude, with the left IFG activation and bilateral SMG activation being selective to the condition-level and trial-level of semantic unification load, respectively. By employing the EEG-fMRI integrated analyses, this study among the first sheds light on how to integrate trial-level variation in language comprehension.