The graph understanding for mastering the natural science concepts through the process skills approach aims to improve student ability in lower secondary school. In this study, we conducted a series of quasi-experiments for participants by using pre-test and post-test. The research instruments consisted of two tests and the questionnaires. After learning through the process skills approach, the post-test was used to evaluate the graph understanding and the mastery of natural science concepts. The aspects of written communication, interpretation, conclusion, and prediction were evaluated for the graph understanding while the aspects of knowledge, comprehension, application, analysis, synthesis, and evaluation were evaluated for the mastery of the concepts. The data were analyzed quantitatively by average scores and level categories. The t-test formula was used with a 5% significance level for the treatment effectiveness. The results showed that the enhancement of graph understanding can increase the concept mastery. The difficulties in understanding the graphs were closely related to the student mastery of prerequisite skills such as the basic concepts of mathematics. Then, the prerequisite skills are very important to improve their knowledge.