Mucopolysaccharidosis type II (MPS II) is an X-linked recessive lysosomal storage disorder resulting from the deficiency of the enzyme iduronate-2-sulfatase (IDS).This study described the molecular characteristics of 63 Chinese children with MPS II and investigated functional characterization of seven novel IDS variants. We analyzed mutations in the IDS gene of 63 children with MPS II. Seven novel mutations were further characterized by transient expression studies. 49 different mutations were identified in the IDS gene including 33 previously reported and 16 novel mutations. The mutation p.R443X and c.1122C > T(p.G374G) may be link to attenuated type. The novel missense mutations were predicted damaging in silico. The bioinformatic structural analysis of the novel missense mutations showed that these amino acid replacements would cause a severe impairment of protein structure and function. In vitro functional analysis of the seven novel mutants, showing a very low IDS activity, clearly demonstrated their pathogenic nature. In western blotting analysis of the IDS protein, the examined mutations showed a similar or slightly lower molecular mass of precursor without mature forms being detected. Our study expands the spectrum of genotype of MPS II, provides new insights into the molecular mechanism of MPS II and helps to the future studies of genotype-phenotype correlations to estimate prognosis and develop new therapeutic approach.