The purpose of the study was to enhance the qualitative teaching of science through affective method. Affective teaching was compared with cognitive teaching of integrated science in the Junior Secondary School. Twenty schools were randomly selected in Ado-Ekiti Nigeria. A sample of 400 Junior Secondary school students, 200 males and 200 females participated in the study 20 items questionnaire tagged Cognitive and Affective Domains Aptitude Test (CADAT) adapted from a standardized test was used to test both the cognitive and affective methods on the learning capacities of the respondents in integrated science t-test was used to analyze the scores. Three Null hypotheses were postulated and tested. Results showed that, there was a significant difference between cognitive and affective achievements of students in science. Hypotheses I was therefore rejected. Hypotheses 2 and 3 indicated no significance gender difference between cognitive and affective test scores. It was concluded that employing affective method in the teaching of integrated science in Nigerian secondary school would enhance the understanding of science more than what is operating now in science classroom. This method could further be experimented at the senior secondary school level.