The purpose of this study was to develop the level-defferentiated Web Based Instruction(WBI) program, to examine its effects on the science achievement self-directed learning characteristics, and the students’ perceptions on the WBI learning. For this purpose, the advanced and complementary WBI program of level-differentiated curriculum was developed to adapt to class fields and examine instruction facilitating efficiency. Designed and developed the WBI program make it possible to teach students according to the level-differentiated learning for the chapter, ‘weather and climate’ in high school science curriculum. The results of this study are as follows: First, level-differentiated WBI was effective to encourage self-concept, learning eagerness, future-oriented self-apprehension, creativity, self-assessment of the student’s self-directed teaming characteristics. There was no interaction effect of treatment and students’ learning ability at the self-directed learning characteristics. Second, the scores of science achievement of WBI group were significantly higher than those of conventional lecture group. There was interaction effect of treatment and students’ learning ability. However level-differentiated WBI has no effect on openness, initiative, responsibility of the student’s self-directed learning characteristics. There was interaction effect of treatment and students’ learning ability at the science achievement, Third, in the perception questionnaire of WBI teaming, many students showed the WBI teaming was good in terms of causing interaction between learners and web based learning materials including various images and animations. However there are several students who showed learning difficulties. For example they wonder which part is more important and what order is proper to study in hypertext environment.