The work reports the structural analysis of a cyanomesogen namely, p-cyanobenzylidene p-nonyloxyaniline belonging to the Schiff base class of compounds. It exhibits a partial bilayer/inter-digitated smectic Ad phase and a nematic phase. Polarising Optical Microscopy (POM) and Differential Scanning Calorimetry (DSC) studies have been carried out to study phase sequence and transition temperatures. Micro-structural parameters, like molecular length, spacing, crystallite size, activation energy and micro-strain, have been estimated and pair correlation function (PCF) studies have been done for exhibited mesophases using the X-ray diffraction technique. The study investigated the surface, electronic and optical properties of a compound by computational studies like Density Functional Theory (DFT) and Hirshfeld surface analysis (HSA) methods using the DFT B3LYP/6-311++G(d,p) level basis set. The results reveal that the polarity associated with the polar groups and alkoxy chain lengths, contributes majorly to the mesomorphic characteristics and stability. The Highest Occupied Molecular Orbitals (HOMO) and Lowest Unoccupied Molecular Orbitals (LUMO) analyses of the DFT optimised molecule give electronic and geometrical parameters, atomic charge distribution, polarisability factors which are used to interpret the characteristics of the mesophases and their suitability for electro-optical and non-linear optical applications of the compound in terms of the predicted data.