Previous studies indicate that wooden environments could produce more positive emotions, more delightful sense of color, odor, light and less fatigue for occupants. The purpose of this study was to examine the gender differences in human psychological responses to three different types of wooden indoor environments. 10 female and 10 male participants were enrolled randomly in the experiment. The Profile of Mood States (POMS), a fatigue symptom checklist was used and some subjective feelings were evaluated. The results showed that: (1) female participants felt more warmth and brightness in the wooden rooms; (2) female participants’ olfactory sensation was 42% higher than male participant in the dark wooden room but experienced a greater decrease after a 50-min adaptation; (3) female participants reported more confusion and fatigue feelings while male participants reported more vigor feelings in different conditions. This study indicated that obvious gender differences existed in human psychological responses to the changes of wooden environment, with different wood colors and coverage rates. It is necessary to think critically about human connections with natural patterns and to improve health and well-being in the built environment with the consideration of gender differences.