Background: In‑flight spatial disorientation (SD) is a predominant threat to flight safety in aviation. This study was conducted to understand the prevalence, severity, and frequency of in‑flight SD among military pilots in Taiwan. Methods: A survey was conducted to collect tri‑service pilots’ experiences of SD during flight. Participants completed anonymous SD questionnaires during refresher physiology training. There were 486 questionnaires delivered to trainees and the completion rate was 97.1% (n = 472). All data were processed using SPSS version 24 software (IBM, Armonk, NY, USA). Results: Of the 472 participants, the average age of the pilots was 36.7 so 7.3 years and 97.7% were male. About 80% of participants experienced in‑flight SD events. There was a significant difference between prevalence of SD in fighter (87.0%), trainer (89.8%), transporter (70.6%), and helicopter (66.7%) pilots (P < 0.001). Less than 10% of the events were severe, and there was no obvious variation between aircraft types (P = 0.126). Pilots were sensitive to SD in clouds and under low visibility. Over 70% of pilots experienced visual illusions, especially loss of horizon during bad weather (45.1%), followed by leans (44.5%), false horizon (44.1%), false sense in clouds (39.6%), Coriolis illusion (25.0%), and confusion on entry to instrument meteorological conditions (25.0%). Conclusions: Our survey showed that SD is a common physiological problem among military pilots, who were easily disoriented by in‑flight SD without visual cues. Visual illusion was relatively more frequent, especially for trainer and fighter pilots.