Soybean is an important protein source for consumers in Taiwan. Soybean production in Taiwan is not self-sufficient. Taiwan imports 2.5 million tons of soybeans annually. More than 90% of the imported soybeans are genetically modified (GM). To provide an objective assessment on safety of GM soybean and for post-market monitoring, we conducted a comparative assessment on key component compositions between imported GM soybean and local non-GM soybean from Taiwan. All the soybean samples were purchased from the local market to simulate the status of Taiwanese consumers in purchasing soybeans. The GM soybean samples were herbicide-tolerant soybeans. The content of the proximate, the amino acid composition, the fatty acid composition, vitamins, minerals, antinutritional factors, and isoflavones of soybean samples were analyzed. Most contents of the key components of the GM soybean had no significant difference with those of the non-GM soybean. However, the contents of ash, crude protein, amino acids, myristic acid, behenic acid, phosphorus, iron and phytic acid were significantly lower in the GM soybean samples, and the contents of crude fat, margaric acid, and stearic acid were significantly higher in the GM soybean samples. But they were all within the range of reference values. A total of 314 pesticide residues in each of the samples were analyzed. Glyphosate residue was detected only in GM soybean samples, but it is well below the threshold prescribed by the government. In summary, the GM soybean samples purchased from Taiwan market were shown to be substantially equivalent to non-GM soybeans.