In a continuous discourse, the importance of information can be conveyed both implicitly and explicitly. Global discourse hierarchy can convey importance implicitly, such that information at higher hierarchy levels is more important than those at lower hierarchy levels. In contrast, focus can mark importance explicitly, with information in focused positions being more important than that in non-focused positions. In this event-related potential study, we investigated whether the processing of implicitly highlighted information and explicitly highlighted information involved different neural mechanisms during online discourse processing. Three-clause discourses were constructed to implement hierarchy manipulation. For the discourses in the high-level condition, the first two clauses were subordinate clauses that formed a sentence, while the last clause formed a sentence independently. Whereas for the discourses in the low-level condition, the first clause formed a sentence independently while the following two clauses formed a sentence together. The last clause of each discourse thus differed in its status in the high and low-level condition and within it a critical word was embedded. For each discourse, a preceding whquestion was added to project a focus position in the discourse so that the critical word was either in the focused or non-focused position. Our results showed that the critical words elicited a smaller N400 when they were located at the higher than at the lower hierarchy level, whereas they elicited enhanced P2 and P3b when they were located in the focused than in the non-focused position. These results suggest that both hierarchy and focus facilitated the integration of highlighted information in the discourse. However, these factors influenced discourse integration in different temporal dynamics and involved different cognitive processes.