Dissolving microneedles are transdermal delivery systems designed to mechanically penetrate the skin and fully dissolve in the skin in a minimally invasive manner. In this study, the skin permeability of compounds encapsulated in microneedles was controlled by changing the composition of microneedle materials. Sodium hyaluronate (SH) and carboxymethyl cellulose (CMC) were chosen as structural materials and amylopectin was used to increase the mechanical strength of microneedles. To determine the effect of microneedle composition on skin permeability, microneedle properties such as mechanical strength and solubility were investigated according to various compositions of SH and CMC. When the CMC fraction in the needle increased, the mechanical strength of the microneedle increased, leading to high skin permeability of rhodamine B, a model compound. Using microneedles, significantly higher skin permeability of niacinamide was also obtained. These results indicate that the microneedles developed in this study improved the skin permeability of compounds loaded in the needle, and the skin permeability could be tuned by changing the composition of microneedle materials.