The ability to read interdisciplinary informational multiple texts is essential—not only as a key factor for students to achieve progressive academic goals, but also as a core competency for entering the workforce, integrating into society, and thriving in the future world. Concept-based inquiry reading instruction promotes conceptual connections and generalization construction across multiple texts. Therefore, this study conducted an instructional experiment on conceptual inquiry in interdisciplinary informational multiple-text reading to examine its effects. A quasi-experimental nonequivalent-group pretest–posttest design was adopted. The independent variable was instructional grouping (experimental vs. control), the pretest served as a covariate, and the dependent variable was students’ scores on interdisciplinary informational multiple-text reading comprehension test. The participants were 105 fifth-grade students from four classes in an elementary school in eastern Taiwan. A nine-week instructional experiment consisting of four units was conducted, comparing the reading comprehension performance between the experimental group, which received concept-based inquiry instruction in interdisciplinary informational multiple texts, and the control group, which received general multiple-text reading instruction. The results indicated that interdisciplinary informational conceptual inquiry-based instruction had positive effects in helping students extract and integrate information, as well as construct concepts and generalizations. The experimental group significantly outperformed the control group in constructing concepts and generalizations in three of the units, and in extracting and integrating information in two of the units. These findings suggest that through inquiry discussions and instruction focused on conceptual thinking across texts, students’ ability to build conceptual connections and construct generalizations in interdisciplinary informational multiple-text reading can be effectively strengthened.