This paper presents a methodology of exergy and thermoeconomic analysis for performance of the Multi-Stage Flash (MSF) process using the developed package. This methodology gets insight on details not available by the first law analysis. The main target of these analyses is to improve the MSF process as well as to determine the unit product cost of the distilled water. Using the developed VDS package, the energy analysis of the considered MSF plant in the rating mode (performance), the gain ratio (GR) is calculated as 7.91. The exergy input, E-F, to the MSF plant is calculated as 10.7 MW which represents the exergy of the heating steam, exergy associated to the sea water feed, and electrical pumping power minus the exergy of the brine heater condensate. Only 0.2 MW of an elevated exergy in the distilled stream is produced. The exergy associated with blow down and rejection of cooling streams is 4.04 MW which nominated as an exergy loss. The remainder part of E-D = 6.46 MW is destroyed internally in the plant components as a result the exergetic efficiency of the considered MSF plant, eta(II) 1.87%. The unit product cost of the MSF desalination plant is calculated as 2.63 $/m(3) by two different ways. The first one by calculating the capital and running costs which invested at the boundary of the MSF plant (input streams); the second way is based on mathematical model (thermoeconornics) by which the outlet streams cost is calculated and charged their value to the desalted water. Thermoeconomic analysis shows that the overall cost of the desalination plant will be obtained if the exergy destruction rate of the desuperheater, the distiller train is reduced. The monetary cost of the streams indicated that any modifications in the first stages will cause more effect other than the last stages. Different partial load conditions for the real data of Eoun Mousa MSF plant are depicted and recorded by Data Control System (DCS). These data are fed to the developed VDS software to investigate the performance of the MSF plant. The distillate product varies from 104 (50%) m(3)/h to 208 (100%) m(3)/h as well as the top brine temperature varies from 86 to 110 degrees C. The heating steam consumption varies from 12 to 26 m(3)/h. Thermocconomic analysis of MSF plant under different partial load conditions showed that the unit product cost increases to 21% when the load decreases to 50% of its design value.