Increased rates of indeterminate QuantiFERON-TB Gold In-Tube (QFT-GIT) results have been reported since the COVID-19 epidemic in Hunan Province, China. The indeterminate result (ITR) rate of QFT increased from an average of 5.2% to 12.4%, paralleling the first COVID-19 pandemic wave in the region. QFT-GIT results of 243 hospitalized patients with COVID-19 from January 2022 to April 2023 at Xiangya Hospital of Central South University were analyzed. Of the 243 patients, 71 (29.2%) had ITRs due to reduced interferon-gamma production in the positive control. Multiple factors are associated with ITRs, such as disease severity, respiratory failure incidence, immunosuppressant use, and prognosis. Additionally, interferon-gamma (Mitogen-Nil) levels differed significantly depending upon disease severity, prognosis, immunosuppressant use, sepsis symptoms, respiratory failure, or hyperlipidemia. An abnormal increase in the ITR rate in the QFT was observed after the COVID-19 pandemic, and an optimal machine learning predictive model for indeterminate QFT results was established.