The purpose of this study was to analyze relationships among science achievement, science process skills and affective perception of high school students. The affective perception was included attitude toward science and science anxiety in the study. The instruments were developed HARS and SAMS for this study. The subject was sampled 1,115 students by stratified cluster sampling method. The major findings of this study were as follows: The tendency to affective perception was investigated according to students variables. Atittude toward science was showed a negative perception on female than male, in rural area than city. Science anxiety was percepted highly on female than male, in rural area than city. Attitude toward science showed positive relations to science process skills, science achievement, but which showed negative relation to science anxiety. Science anxiety showed negative relations among science process skills, science achievement and attitude toward science. Structural relationships among affective perception, science process skills and science achievement were analyzed by effect size through the path analysis on the independent and dependent variables. By the results, it was indicated that there have significant direct effect not only affective perception influence on science achievement but also on science process skills in hypothesized model. Prediction of science achievement and science process skills were clarified to characteristics of the affective perception.Therefore, understanding about affective perception will be helpful to make the strategy of science teaching