We examined explicit processing of musical syntax and tonality in a group of Han Chinese Mandarin speakers with congenital amusia, and the extent to which pitch discrimination impairments were associated with syntax and tonality processing. In Experiment 1, we assessed whether congenital amusia is associated with impaired explicit processing of musical syntax. Congruity ratings were examined for syntactically regular or irregular endings in harmonic and melodic contexts. Unlike controls, amusic participants failed to explicitly distinguish regular from irregular endings in both contexts. Surprisingly, however, a concurrent manipulation of pitch distance did not affect the processing of musical syntax for amusics, and their impaired music-syntactic processing was uncorrelated with their pitch discrimination thresholds. In Experiment 2, we assessed tonality perception using a probe-tone paradigm. Recovery of the tonal hierarchy was less evident for the amusic group than for the control group, and this reduced sensitivity to tonality in amusia was also unrelated to poor pitch discrimination. These findings support the view that music structure is processed by cognitive and neural resources that operate independently of pitch discrimination, and that these resources are impaired in explicit judgments for individuals with congenital amusia.