A controllable length of inorganic nanotubes as a drug delivery system is crucial to understanding internalization mechanisms and designing new biomedical applications. In this study, silica nanotubes (SiNTs) with controlled length ranging from several hundred nanometers to several micrometers were firstly fabricated via a facile and effective acid-degradation collagen template route and then functionalized with chitosan (ChSiNTs) to deliver immunostimulatory cytosine-phosphodiester-guanine oligodeoxynucleotides (CpG ODNs). It was found that the length of SiNTs could be well controlled through the adjustment of the acid-treatment temperature. Cytotoxic assessment indicated that SiNTs exhibited good biocompatibility when separately incubated with four types of cell lines: 293XL-hTLR9, A549, NIH3T3, and C2C12. The cellular uptake of SiNTs was strongly affected by their length and cell type. A decrease in the length led to an increase in the cellular uptake of SiNTs, while a significantly higher cellular uptake by C2C12 cells was observed in comparison with A549 and NIH3T3 cells. An immunochemical assay revealed that SiNTs were located in the endolysosomes after cellular internalization. ChSiNTs were positive and well complexed with negative CpG ODNs to produce a ChSiNT/CpG ODN complex (CpG-ChSiNT) via electric force. ChSiNTs were located in the endolysosomes after internalization and enhanced the cellular uptake of CpG-ODNs. CpG ODNs could be released from CpG-ChSiNTs in a sustained way and specifically recognized by the TLR9 receptor in 293XL-hTLR9 cells. The amount of interleukin-6 cytokine stimulated by CpG-ChSiNT against peripheral blood mononuclear cells was higher than that by free CpG ODNs and ChSiNTs significantly enhanced the immunostimulatory response of CpG ODNs.