Mesoporous silica nanoparticles (MSNs) have been widely used in biomedical applications. However, most studies have been limited to spherical MSNs, while non-spherical MSNs have never been rigorously studied. In this study, we fabricated mesoporous silica nanospheres (MSNSs) and mesoporous silica nanorods (MSNRs), with different aspect ratios (ARs) but identical surface chemistries to explore the shape effects of MSNs on oral delivery. The results of cellular studies demonstrated that MSNRs exhibited a higher cellular uptake than MSNSs. Mechanistic studies showed that caveolae-mediated endocytosis was involved in the uptake of MSNRs, while the clathrin-dependent pathway contributed to the endocytosis of MSNSs. Meanwhile, the apparent permeability coefficient value (P) of doxorubicin hydrochloride (Dox)-loaded MSNRs was approximately 1.8-, 3.2- and 6.3-fold higher than that of Dox-loaded MSNS1, Dox-loaded MSNS2 and Dox solution, respectively. The in vivo pharmacokinetics study showed that the area under the plasma concentration-time curve (AUC) achieved by Dox-loaded MSNRs was 1.9-, 3.4- and 5.7-fold higher than the corresponding values for Dox-loaded MSNS1, MSNS2 and Dox solution, respectively. Taken together, our results demonstrated that tuning nanoparticle shape potentially determines the biological fate of nanoparticles with higher delivery efficiency, such as enhanced cellular uptake and oral bioavailability.