This present work introduces a novel thiomer/nanoclay nanocomposite material with mucoadhesive and controlled release properties that has been prepared and evaluated as a potential drug carrier system. This hybrid material is based on thiolated alginate and organically modified montmorillonite (MMT). Alginate thiomer was synthesized by immobilization of l-cysteine on alginate backbone via carbodiimide reaction. Thiol/disulfide groups were identified and quantified by FT-IR, 1H NMR and Ellman's method. Rheological assays as preliminary in vitro mucoadhesion test using mucin show that complex viscosity increases until ∼7-fold compared to unmodified alginate/mucin, and G’ > G″ is present in thiomers, compared with G” > G′ present in unmodified alginate, which indicate strong interactions between thiomer and mucin. Thiomer/nanoclay nanocomposites were prepared by film casting method and characterized by TGA, XRD, TEM and rheometry. Nanocomposites maintain rheological properties showed by thiolated alginate when they are tested with mucin, increasing complex viscosity until ∼8-fold respect a nanocomposite formulation based on unmodified alginate. The release of deltamethrin from nanocomposite films was studied and the impact of the amount of nanoclay (0–7%) and four types of organic modifiers in MMT were evaluated. Different kinetic models were evaluated in order to study the mechanism involved in drug release. Zero, first, Higuchi and Korsmeyer-Peppas model were evaluated, being the last two kinetic models the ones with better fitting and higher values of R2. The presence of nanoclay on the formulation influence significantly (P < 0.001) deltamethrin short-term release showing an anomalous and Case-II transport mechanism. Compared with a Fickian diffusion when nanoclay is absent in the formulation. The diffusion coefficient D could decrease until ∼7-fold compared to a formulation without nanoclay. Long-term release is significantly influenced (P < 0.0001) by the chemical nature of organic modifier used on nanoclay and its interaction with the drug. This thiomer/nanoclay nanocomposite material could be a useful prospect as a mucoadhesive material for drug carrier with controlled drug release properties.