Natural convective flows are commonly found in nature around us in our day-to-day life such as in atmospheric and oceanic flows, electronic cooling, and building ventilation. Studying such flows within enclosures can provide important information about flow field which can help to explain transport of neutrally buoyant bio-aerosols, contaminants, etc. In this study, linear stability analysis of two-dimensional steady base flow inside a square cavity is carried out by considering three-dimensional disturbances. The 2D base flow has been numerically computed over the range of Rayleigh number, \({\text{Ra}} = 10^{4}{-}10^{5}\) , Prandtl number, \({\text{Pr}} = 0.71\) (air). The evolution equations of the perturbations have been obtained using linear stability theory, and using normal mode form of solution leads to a generalized eigenvalue problem (EVP). A mixed finite element P2-P1 spatial discretization was used to solve both the base flow and EVP. Temporal stability analysis was carried. The eigenspectrum for a particular case ( \({\text{Ra}} = 10^{4}\) , wave number = 1) is studied. In the parameter range \({\text{Ra}} = 10^{4}{-}10^{5}\) , the critical flow parameters, Ra values and corresponding wave numbers, at which the flow loses stability are determined.