Transdermal delivery through the skin barriers is an important medical procedure to transfer drugs into the human body. However, there is an urgent requirement to design microneedle‐based transdermal delivery systems with superior delivery efficiency, low toxicity, excellent mechanical property, and simple synthetic process. Herein, perpendicular calcite microneedle arrays with a length of about 8 µm are synthesized on the prism layer of mollusk shells via oriented dissolution while dextran sulfate sodium is applied as an additive. Ordered patterns of long calcite microneedles with a length about 45 µm are synthesized in a large scale for the first time on mollusk prism layers via oriented dissolution while circular masks are covered on the prism layers during the dissolution process. The long calcite microneedle arrays with the ordered pattern are found to be efficient for transdermal delivery of dexamethasone and for therapy of ear psoriasis in mice. The calcite microneedle arrays are also applied to transport Cy3 fluorescent biomolecules through cell membranes in this work. These calcite microneedle arrays can be applied as efficient transportation substrates for both transdermal and intracellular delivery, which exhibit advantages such as high drug loading capacity, superior biocompatibility, nontoxicity, high mechanical properties, and easy synthesis strategy.