Confined liquids exhibit altered molecular alignment, layered and/or multistage phase transitions, shifted freezing/melting behavior, and structurally distinct polymorphs compared to their bulk counterparts. This dissertation explores how nanoconfinement modifies the structural and dynamic evolution of water, hydrocarbons, and their mixtures using a combination of thermal analysis and molecular dynamics (MD) simulations. In Chapter 2, the layered freezing of water in mesoporous silica is quantified as a function of pore size and pore filling, revealing discrete structural regions, weak first-order transitions, and distorted ice polymorphs. These behaviors arise from strong hydrogen bonding at the silica surface, which stabilizes interfacial unfrozen water layers and drives sequential freezing. Chapter 3 establishes a robust methodology for studying confined water–oil mixtures using n-decane as a model system. It demonstrates that strong water–silica interactions lead to a core–shell structure where water encapsulates oil, suppressing n-decane’s phase transitions and reorganizing the interfacial structure. The molecular alignment of encapsulated n-decane is influenced by both water–oil interactions and the relative size of confinement compared to the molecules. Chapter 4 investigates the odd–even effect in normal alkanes and finds that hydrated confinement selectively restores rotator phases in odd-numbered chains such as n-undecane and n-tridecane. This recovery is enabled by the combined effect of repulsive water–hydrocarbon interactions and enhanced molecular freedom due to unfrozen water. Chapter 5 broadens the study to branched alkanes, cyclic hydrocarbons, and aromatic compounds. It reveals that increasing molecular complexity enhances freezing point depression and suppresses long-range ordering. These effects are governed by steric hindrance, disrupted packing efficiency, and confinement-induced geometric frustration, which collectively weaken crystallization in confined environments. Chapter 6 explores hydrophobically functionalized silica, where the absence of interfacial hydrogen bonding reverses spatial partitioning. Here, n-decane migrates toward the pore wall while water is confined centrally, highlighting how surface chemistry reshapes molecular organization and phase behavior. These findings deepen our understanding of confined-phase transitions and offer molecular-level insights for designing advanced materials in energy, environmental, and chemical applications.