Purpose: Reading difficulty (RD) affects 5–10% of the population across languages (Wagner in J Learn Disabil 53(5), 354–365, 2020). However, only a few studies have focused on developing effective interventions for Chinese children with RD. Both the phonological deficit and morphological deficit hypotheses have been proposed to explain the underlying cognitive cores of RD in Chinese, with limited research directly comparing the interventions targeting these skills. Method: In the current study, we designed and directly compared a phonological and a morphological training program in improving reading for Chinese children with RD. The phonological training program addressed phonological awareness and conversion from orthography to phonology, while the morphological training addressed morphological awareness and conversion from orthography to meaning. Sixty-two fifth-grade students with RD were randomly assigned to the phonological, morphological intervention, or a business-as-usual (BAU) group. Results: Both the phonological training (PT) and the morphological training (MT) improved sentence reading fluency, character naming, one-minute irregular character naming, and phonological awareness compared to the BAU group. Furthermore, we found that responsiveness to the PT was negatively correlated with phonological awareness and maternal education, while responsiveness to the MT was positively correlated with rapid automatized naming (RAN) skills. Conclusion: The phonological training and the morphological training had similar effectiveness in promoting reading in Chinese children with RD, which provides important insights into reading intervention for Chinese RD.