This study applied the Porter's alignment model to construct a localized two-dimensional framework based on Anderson's taxonomy. The research chose the third-grade primary school science textbooks from two representative presses in China and Japan, coded the textbooks and curriculum standards, calculated the alignment level between the textbooks of the two presses and their corresponding curriculum standards, and discussed the alignment level from the topic, cognitive demand, and emphasis. The results show that the B version in Japan is significantly aligned with the Japanese curriculum standard, but the A version in China does not have significant alignment with the Chinese curriculum standard. Besides, a common problem is that the ratios of life science in sample science textbooks both exceed the requirements of the curriculum standards, and the problems of exceeding the standard in cognitive demand and not highlighting the key points also need to be concerned. This study provides ideas and references for countries with similar educational situations to study the compilation of science textbooks and fills up the deficiency of the international comparison of the alignment between primary school science textbooks and curriculum standards by using the alignment model.