Background: Revealing clinical manifestations and associations of COVID-19 before and after negative transition remains an area of significant uncertainty. The aim of this study is to investigate clinical characteristics observed during and after Omicron infection among healthcare workers (HCWs). Methods: From November 4, 2022 to January 15, 2023, HCWs in our hospital were enrolled to document clinical symptoms, prevention, and treatment for COVID-19 using structured questionnaire. Results: Out of the 1101 HCWs included, SARS-CoV-2 infection was detected in 78.20% (861/1101) during observation period. Nucleic acid conversion took a median duration of 8 days. Forty-three symptoms were identified during SARS-CoV-2 infection (11 symptoms per individual). These symptoms can be further categorized into five groups: fever, upper respiratory tract, influenza, digestive, and systemic; all showing complex and diverse patterns. Following SARS-CoV-2 infection, a total of 19 symptoms were recorded including four newly emerged ones: reduced lung capacity, memory loss, lethargy and inattention. Importantly, we observed a significant association between gastrointestinal symptoms during the nucleic acid positive phase and subsequent neuropsychiatric manifestations after negative conversion. Conclusions: The clinical manifestations observed in HCWs during and after Omicron infection displayed intricate patterns, shedding new light on the complex interplay between SARS-CoV-2 and human.