Substantial evidence revealed that morphological awareness could contribute to reading achievement in different alphabetic languages among children with and without reading difficulties. However, as the most spoken non-alphabetic language, there is a paucity of available research on Chinese reading development and impairment. This research focused on evaluating two potential intervening variables through the relationship between morphological awareness and reading comprehension. Compounding awareness, homophone awareness, homograph awareness, in addition to reading ability including character recognition, vocabulary knowledge, and reading comprehension were assessed in this research. Controls of phonological awareness and rapid automatized naming (RAN) were also included in the model. Participants were 200 second-grade students with reading difficulties in Chinese mainland . Path analysis revealed that morphological awareness made a direct contribution to reading comprehension beyond all other variables and this relationship was mediated by character recognition and vocabulary knowledge. Furthermore, two indirect pathways showed a significant difference in this study. The distinctive role of morphological awareness in reading comprehension for Chinese children with reading difficulties and the potential reasons for the significant effect difference between the two indirect pathways were discussed at the end of the study.