Host specificity of parasitoids may be measured by various specialization indices to assess the variation of interaction strength among species and the structure of the wider interaction network. However, the conclusions from analyses at the species and network levels may differ, which remains poorly explored. In addition, the recovery of cryptic species of hosts and parasitoids with molecular data may affect the structure of inferred interaction links. We quantified host specificity of hymenopteran parasitoids (family Encyrtidae) on armored scale insects (Hemiptera: Diaspididae) from a wide geographic sampling range across the Chinese Mainland based on both morphological and molecular species delimitation. Mitochondrial COI and nuclear 28S markers detected high cryptic species diversity in the encyrtids and to a lesser degree in the diaspidids, which divided generalist morphospecies into complexes of specialists and generalists. One-to-one reciprocal host–parasite links were increased in the molecular data set, but different quantitative species-level indices produced contrasting estimates of specificity from various one-to-multiple and multiple-to-multiple host–parasite links. Network indices calculated from DNA-based species, compared to morphology-based species definitions, showed lower connectance and generality, but greater specialization and compartmentalization of the interaction network. We conclude that a high degree of cryptic species in host–parasitoid systems refines the true network structure and may cause us overestimating the stability of these interaction webs.