Most behavioral interventions on reading disability (RD) have been developed in alphabetic languages and are phonologically-based. Chinese is a morpho-syllabic language in which each character represents a morpheme and a syllable. Therefore, phonologically-based interventions may not be most helpful in Chinese. In this study, we compared a phonological and a morphological intervention (MI) in Chinese children with RD both behaviorally and neurologically. We recruited 80 fifth-grade Chinese children, including 18 typically developing children as age controls (AC), and 62 children with RD, 22 of whom received the phonological intervention (PI), 22 of whom received the MI, and 18 served as waiting-list controls (WL). An auditory rhyming task and a visual spelling task were employed to examine brain activation before and after the intervention. We found that the PI and MI both effectively improved character naming, sentence reading fluency, one-minute irregular character reading and phonological awareness compared with the WL group. At the brain level, the PI group showed greater increase of brain activation in the right middle temporal gyrus than the MI and WL following the intervention in an auditory rhyming task, suggesting compensatory phonological strategies developed in PI. The MI group showed greater increase of brain activation in the left middle frontal gyrus, left inferior frontal gyrus and left fusiform gyrus than the PI and the WL group following the intervention in a visual spelling task, suggesting functional normalization, because these regions were less activated in children with RD than typical controls before the intervention. These findings suggest intervention-specific brain changes with otherwise similar effectiveness in the behavior. It provides important insights in understanding brain mechanisms underlying behavioral intervention in children with RD.