Background: In recent years, several versions of the Abbreviated Injury Scale (AIS) were updated and published. It was reported that the codeset in the dictionary of AIS-2005 had significant change from that of AIS-1998. This study was designed to evaluate the potential impact of adapting the AIS-2005 codeset from the AIS-1998 in an established trauma system of a single level I trauma center. The patients’ outcome was measured in different Injury Severity Score (ISS) strata according to the double-coded injuries in a three-year period. Methods: The double-coded injuries sustained by 7520 trauma patients between 1 January, 2016, and 31 December, 2018, in a level I trauma center were used to compare the patient injury characteristics and outcomes between AIS-1998 and AIS-2005 and under different ISS strata, defined as <16 (mild to moderate injury), 16–24 (severe injury), and >24 (critical injury). Results: The mean ISS was significantly lower using AIS-2005 than using AIS-1998 (7.5 ± 6.3 vs. 8.3 ± 7.1, respectively, p < 0.001). AIS-2005 scores in the body regions of the head/neck (2.94 ± 1.08 vs. 3.40 ± 1.15, respectively, p < 0.001) and extremity (2.19 ± 0.56 vs. 2.24 ± 0.58, respectively, p < 0.001), but not in other body regions, were significantly lower than AIS-1998 scores. The critically injured patients (ISS >24), but not severely injured patients or patients with mild-to-moderate injury, coded by AIS-2005 had a significantly higher mortality rate (34.2% vs. 26.2%, respectively, p = 0.031) than did patients coded by AIS-1998. The rate of intensive care unit admission was significantly higher for patients in all ISS strata after adapting AIS-2005 as the scoring system than after adapting AIS-1998. Regarding patients with major trauma, which was defined as ISS > 15, the number of patients with major trauma in this study was 17.0% (n = 1276) for AIS-1998 and 9.7% (n = 733) for AIS-2005. As a consequence, the mortality rate of patients with major trauma was significantly higher in AIS-2005 than in AIS-1998 (15.4% vs. 9.1%, respectively, p < 000.1). Conclusions: In this study, we revealed that the adaptation of AIS-2005 from AIS-1998 had resulted in a significant decrease of severity scores in the measurement of the same injuries. The number of head/neck injuries classified as 16–24 was the key difference between AIS-1998 and AIS-2005. Furthermore, critically injured patients who had ISS > 24 coded by AIS-2005 had significantly higher mortality rates than did the patients coded by AIS-1998. This study also indicated that a direct comparison of the measurements that are generated from these two AIS versions can produce misleading results.