The purpose of this study was to investigate whether a virtual reality (VR) program designed and developed based on the hallucinogenic harm reduction and integration (PHRI) clinical model could be more effective in guiding positive thinking training, improving positive thinking awareness and ability, and, to some extent, facilitating personal efficacy and emotional state compared to a traditional VR program that places users in a virtual natural ecological environment to guide positive thinking training. We also sought to understand the factors that may influence the effectiveness of VR interventions and user experience. Seventy-six randomly recruited participants were divided into a control group and an experimental group of 38 participants, each according to a random number table, and were trained in VR meditation for eight weeks. The experimental group used a PHRI-based mindfulness program, while the control group used a traditional mindfulness meditation program. We used The Mindful Attention Awareness Scale and the PAD emotional three-dimensional scale to assess the level of state mindfulness and changes in the emotional state before and at the end of the experiment. The Immersive Tendencies Questionnaire measured the user's sense of presence and immersion in the virtual environment. The Five Facet Mindfulness Questionnaires and the Depression Anxiety and Stress Scale (DASS-21) were used at the baseline assessment stage before and at the 4-week follow-up after the experiment to assess the change in trait mindfulness levels due to the mindfulness training. The Five Facet Mindfulness Questionnaires and the DASS-21 were used to assess changes in mindfulness and mental health trait levels. At the end of the experiment, the MMSQ score was significantly lower in the control group than in the experimental group, while the ITQ score was significantly higher than in the experimental group, and both scores were statistically significant (p < 0.05). In the follow-up assessment four weeks after the end of the experiment, the FFMQ-15 score and the DASS-21 were significantly and statistically higher in the experimental group than in the control group (p < 0.05). Since the scores of the PAD scale did not obey a normal distribution, we used the Wilcoxon signed-rank test to assess the results, which proved that the experimental group had higher levels of emotional activation and arousal. The VR positive thinking program developed based on PHRI can significantly increase the positive thinking state and emotional arousal and activation of the general population participants but does not directly lead to the growth of positive emotions. Moreover, this detached psychedelic scene brings users a weaker sense of presence and presence than traditional natural space scenes. Furthermore, it does not bring any intense simulator motion sickness symptoms. These findings suggest that VR programs developed based on PHRI have a more positive facilitation effect on the positive state and that this increase lasts longer than conventional VR-positive programs.