Carbon nanotubes (CNTs) catalyzed activation of peroxides has been extensively investigated, while the role of residual metal species in CNT in the catalysis is largely overlooked. In the study, calcination treatment of pristine CNT at high temperatures was employed as an approach to gain an insight into the role of residual metal species as catalytic sites in promoted catalytic activation of periodate (PI). Firstly, the calcination treatment at 500–1100 °C significantly promoted PI activation by calcined CNT. By constructing the quantitative structure–activity relationships (QSARs) between several surface and bulk properties of CNT (such as total surface oxygen content, surface carbonyl group, bulk defect and residual metal species) and PI activation performance, the residual metal species were identified as the catalytic sites. Moreover, the purification method of pristine CNT in the concentrated HNO3 was confirmed to be not efficient to remove these residual metals. The calcination treatment can tune the electronic structure of residual metal species, and promote their exposure and electron donation capacity for PI activation, thus significantly improving PI activation performance. Moreover, IO3• was identified as the dominant reactive species in CNT/PI system via a line of approaches including quenching experiments, PI decomposition in the presence/absence of organic pollutants, electrochemical testes, high selectivity in degradation of organic pollutants, QSARs of substituted phenols, and analysis of degradation products of 4-bromophenol. Furthermore, the CNT/PI system exhibited a wide pH application range of 3–11, high anti-interference to bicarbonate, chloride and phosphate in water. The study advances the understanding on the residual metal species in CNT and its overlooked catalytic role in PI activation, and also provides a high-performance oxidation process for wastewater purification.