Although the connection between the left inferior frontal gyrus (LIFG) and the left superior temporal gyrus (LSTG) has been found to be essential for the comprehension of relative clause (RC) sentences, it remains unclear how the LIFG and the LSTG interact with each other, especially during the processing of Chinese RC sentences with different processing difficulty. This study thus conducted a 2 × 2 (modifying position × extraction position) factorial analyses to examine how these two factors influences regional brain activation. The results showed that, regardless of the modifying position, greater activation in the LIFG was consistently elicited in Chinese subject-extracted relative clauses (SRCs) with non-canonical word order than object-extracted relative clauses (ORCs) with canonical word order, implying that the LIFG subserving the ordering process primarily contributes to the processing of information with increased integration demands due to the non-canonical sequence. Moreover, the directional connection between the LIFG and the LSTG appeared to be modulated by different modifying positions. When the RC was at the subject-modifying position, the effective connectivity from the LIFG to the LSTG was dominantly activated for sentence comprehension; whereas when the RC was at the object-modifying position thus being more difficult, it might be the feedback mechanism from the LSTG back to the LIFG that took place in sentence processing. These findings reveal that brain activation in between the LIFG and the LSTG may be dynamically modulated by different processing difficulty and suggest the relative specialization but extensive collaboration involved in the LIFG and the LSTG for sentence comprehension.