This study aimed to investigate the meta-linguistic and executive function profile for different subtypes of reading difficulties (RD) among upper-elementary students. Based on 1,112 third- to fifth-grade Chinese-speaking children, we identified 72 with decoding difficulties (DD), 74 with comprehension difficulties (CD), and 29 reading-level-matched typically developing (R-TD) peers. All children were assessed on four meta-linguistic measures (phonological awareness, morphological awareness, rapid automatized naming, and orthographic awareness) and three sets of four executive function measures (working memory, inhibition, switching, and updating) in numerical, verbal, and visuospatial domains, respectively. Results showed that compared with R-TD peers, DD showed comprehensive meta-linguistic deficits, whereas CD was related to deficits in morphological awareness. Both DD and CD groups had extensive executive function deficits across numerical, verbal, and visuospatial domains. Notably, CD showed more severe deficits on visuospatial executive function than DD. Structural equation modelling showed the executive function differences between DD and R-TD peers were partially explained by meta-linguistic skills; however, executive function deficits and meta-linguistic deficits were relatively independent in CD. These findings suggested DD and CD are distinctive RD subtypes among Chinese students. Morphological awareness deficit is the core and consistent meta-linguistic deficit among Chinese RD, while visuospatial executive function deficit is the important marker of Chinese CD. Implications for the identification and instructions of different subtypes RD for Chinese students were discussed.