To achieve successful communication, people should decode not only the literal meaning of an utterance, but also the intended meanings conveyed by the speaker. In the present study, event-related potential (ERP) technique was used to explore how working memory capacity modulates the processes of indirect replies comprehension. Conversations of Speaker A and Speaker B were constructed. Speaker A’s question renders Speaker B’s reply to be either direct or indirect replies. Participants of high and low working memory span were instructed to read for comprehension. Our results showed that for the high span group, indirect replies elicited a larger P200, a larger P300 and a larger delayed Late Positive Component (LPC) compared with direct replies. While for the low span group, only a delayed LPC effect was elicited by indirect replies. These findings provide evidence that readers’ working memory capacity modulates the early detection and immediate processing of indirect replies.