Hydrogel is a three-dimensional cross-linked hydrophilic network that can imbibe a large amount of water inside its structure (up to 99% of its dry weight). Due to their unique characteristics of biocompatibility and flexibility, it has found applications in diversified fields, including tissue engineering, drug delivery, biosensors, and agriculture. Even though hydrogels are widely used in the biomedical field, their lower mechanical strength still limits their application to its full potential. Hydrogels can be reinforced with organic, inorganic, and metal-based nanofillers to improve their mechanical strength. Due to improved computational power, computational-based techniques are emerging as a leading characterization technique for nanocomposites and hydrogels. In nanomaterials, atomistic description governs the mechanical strength and thermal behavior that realized atomistic level simulations as an appropriate approach to capture the deformation governing mechanism. Among atomistic simulations, the molecular dynamics (MD)-based approach is emerging as a prospective technique for simulating neat and nanocomposite-based hydrogels' mechanical and thermal behavior. The success and accuracy of MD simulation entirely depend on the force field. This review article will compile the force field employed by the research community to capture the atomistic interactions in different nanocomposite-based hydrogels. This article will comprehensively review the progress made in the atomistic approach to study neat and nanocomposite-based hydrogels' properties. The authors have enlightened the challenges and limitations associated with the atomistic modeling of hydrogels.