This study develops virtual manipulative, polyominoes kits for junior high school students to explore polyominoes. The current work conducts a non-equivalent group pretest-post-test quasi-experimental design to compare the performance difference between using physical manipulatives and virtual manipulatives in finding the number of polyominoes. Sixty eighth-grade students from two different classes in a junior high school in Taipei County of Taiwan participated in this study. The current research randomly selected one class as the experiment group and the other as the control group. Students in the experiment group used virtual manipulatives to explore polyominoes and those in the control group used physical manipulatives. The results revealed that learning in the experiment group is as effective as that in the control group. This study identifies two obvious strategies (add one and reduce) among students in both groups. New ideas, including using new symbols to record the results and considering the influence of symmetry and rotation on the figures, occurred in the virtual manipulative group. Students in the virtual environment paid much more attention to exploring the polyomino problem.