Different cooking methods were effects on the fatty acids and food nutritional qualities. Fish is the most nourished food containing a higher ratio of essential fatty acids. This study is contacted to determine the effect of different cooking methods (microwaving, boiling and grilling) for preparing salmon, mackerel, sardine and tuna had on the fatty acid profiles, in particular the ω-3 fatty acid. Depending on estimated polyunsaturated/saturated ratio and ω-6/ ω-3 ratio as a measure of the propensity of the fish and cooked fish to influence the incidence of coronary heart disease indices of atherogenicity and thrombogenicity which were identified nutritional benefit from fish lipid. Also determine the level of minerals and toxic contaminant in fish meat according different cooking methods. Study was carried on salmon, sardine, mackerel and tuna fishes. The samples were cooking by different methods. These were microwaving, grilling and boiling. By lipid extraction, fatty acids profile was determined in all fresh and processed fish. From the fatty acid profile, the atherogenicity index (AI) and thrombogenicity (TI) indices were calculated. Mineral and toxic hazardous mineral were also identified in the cooked fish. It could be concluded that the use of heating process of fish especially microwave is advantageous over conventional cooking like grilled and blanched fish especially with salmon and mackerel. It also, the ω3 fatty acids retarded the decline in cognition over time. So, then ω-3 also produces a potent anti-thrombotic effect by decreasing production of thromboxane. There is evidence that the type of fat is more important than the total amount of fat in the quantification of cardiovascular disease risk; therefore, the Atherogenicity Index (AI) and the thrombogenicity Index (TI) were also evaluated. Using grilling and boiling process in the most of the fishes were able to decrease the level of cadmium in all studied fish.