Current research shows that consuming high-fat and salt that are now the main ingredients of modern diets over a period of time can disrupt the gut ecosystem, leading to metabolic imbalances and metabolic diseases. However, which component of modern diets, such as high-fat and high-salt consumption for a short duration, is more harmful to health based on its impact on gut bacteria and associated health outcomes is still poorly explored. This study aimed to determine which of high fat or high salt is more detrimental to health by feeding mice HFD and HSD diets for a short period of 3 weeks. To address these wide knowledge gaps, we conducted a high-throughput sequencing study to see how gut microbiota profile changes in HFD or HSD-fed mice. Further, we also investigated whether high fat or high salt is more detrimental to health. In this study, the mice were fed a standard chow diet (CD), HFD and HSD for 3 weeks. Animals were euthanized and examined of haemato-biochemical and histopathological attributes. We also used 16S rRNA sequencing followed by bioinformatics analysis to evaluate the changes in gut microbiota ecology. Interestingly, this study found that HFD or HSD feeding for a short duration induces the pathophysiological attributes of a typical metabolic syndrome as indicated by serum biochemistry and significantly modifies gut microbiota in mice. We concluded that HSD causes significantly more changes in gut bacteria than HFD due to a diminution of beneficial gut bacteria and an enrichment of harmful gut bacteria. We found that HFD led to a more significant increase in plasma total cholesterol (TC), a known risk factor for heart disease, stroke, and atherosclerosis. While HSD is more detrimental to the kidneys, since an increase in creatinine levels indicates kidney disease. Furthermore, mice fed HFD or HSD for a short duration showed minimal and insignificant pathological changes in their hearts, livers, and kidneys.