Research was conducted to observe the effect of Number of Transparent Covers and Refractive Index on performance of a domestic Solar Water heating system. The enhancement of efficiency for solar thermal system is an emerging challenge. The knowledge gained from this research will enable to optimize the number of transparent covers and refractive index prior to develop a solar water heater with improved optical efficiency and thermal efficiency for the collector. Numerical simulation is conducted on the performance of the liquid flat plate collector for July 21st and October 21st from 8 am to 4 pm with different refractive index values 1.1, 1.4, 1.7 and different numbers of transparent covers (0-3). In order to accomplish the proposed method the formulation and solutions are executed using simple software MATLAB. The result demonstrates efficiency of flat plate collector increases with the increase of number of covers. The performance of collector decreases when refractive index is higher. The improved useful heat gain is obtained when number of cover used is 3 and refractive index is 1.1.