Objectives: Gastro-esophageal reflux disease (GERD) is a common disease in gastroenterology outpatients. However, some patients with typical reflux symptoms does not satisfy diagnostic criteria. This study was to explore the value of adjunctive evidence from multichannel intraluminal impedance-pH (MII-pH) monitoring and esophageal high-resolution manometry (HRM) in inconclusive GERD patients with acid exposure time (AET) 4–6%. Methods: Endoscopy, MII-pH monitoring and esophageal HRM were retrospectively analyzed from consecutive patients with typical reflux symptoms in a tertiary hospital from 2013 to 2019. Patients were categorized as conclusive or inconclusive GERD according to AET. Adjunctive evidence for GERD diagnosis from Lyon Consensus were collected and analyzed. Results: Among 147 patients with typical reflux symptoms, conclusive GERD was found in only 31.97% of patients ( N = 47). The remaining 100 patients (68.03%) were inconclusive GERD, of whom 28% ( N = 28) had AET 4–6%. These patients suffered similar reflux burden and impaired esophageal movement. Inconclusive GERD patients with AET 4–6% had lots of positive adjunctive evidence from HRM and MII-pH monitoring. In receiver operating characteristic analysis, mean nocturnal baseline impedance (MNBI) and post-reflux swallow-induced peristaltic wave index (PSPWI) had an area under the curve (AUC) of 0.839 (CI: 0.765–0.913, p < 0.001) and 0.897 (CI: 0.841–0.953, p < 0.001), respectively, better than total reflux episode (AUC of 0.55, p = 0.33). When MNBI was combined with PSPWI, the AUC was elevated to 0.910 (CI: 0.857–0.963, p < 0.001). Conclusions: Inconclusive GERD patients with AET 4–6% have similar acid burden and esophagus motility dysfunction to GERD patients. MNBI and PSPWI are pivotal adjunctive evidence for diagnosing GERD when AET is borderline.