Because the embedded computer performance evaluation indexes are uncertainty, the better method of embedded computer performance evaluation is proposed by applying the set pair analysis theory. First, identical degree, different degree, and contrary degree are respectively determined by the optimal program, intermediate program and worst program, and the weight of performance evaluation indexes are determined by order relation analysis. Finally, the weight contact coefficient is obtained, and the sort of embedded computer performance is determined by situation of weight contact coefficient. The experimental results show that this method can effectively evaluate the embedded computer performance, and the evaluation results are in line with the actual situation.