Many researchers claim that inquiry-based learning offers proper solutions to engage students in the 3D virtual world (3DVW), while little literature has reported how to conduct inquiry-based learning and to what extent it influences learning in this world. This study investigates the perceived effectiveness when students exhibit in the inquiry-based learning compared with the standard learning in the 3DVW. Forty-eight students voluntarily participate in the experiment. Half of them learn in the inquiry-based environment, and the other half learn in the standard environment. The effectiveness is measured by the perceived experience and perceived knowledge gains. The data is analyzed by combining the quantitative with qualitative approaches. The results show students who exhibit in the inquiry-based environment perceive more effectiveness than those who don’t. Also, the reasons why students perceive in the way are obtained. This study indicates the inquiry-based learning conducted in the 3DVW can effectively enhance learning.