The global pandemic of coronavirus disease 2019 (COVID-19), caused by the spread of the respiratory virus, SARS-CoV-2, challenged all countries in disease control. While many countries implemented lockdowns, Japan shortened business hours and issued non-binding public health recommendations without lockdowns. Although Japan has the second largest aging population in the world, the cumulative confirmed COVID-19 deaths per capita were reportedly 10 to 40 times lower than the United States and United Kingdom from 2021 to 2022. Person-to-person interactions can impact the spread of respiratory infections. Social contact surveys provide crucial insights into these behaviors during epidemics. This PhD thesis focused on two aims: 1. Collect data on contact patterns relevant to disease transmission using social contact surveys in Japan. 2. Explore the role of contact patterns and other factors in disease transmission through mathematical modeling. In Japan, the mean number of contacts in 2021–2023 reduced by 50% compared to prepandemic times. Once governmental measures were relaxed, both frequency and duration of contacts increased gradually, but increased contacts were associated with longer hours of mask wearing, denoting a generalized cautiousness of the population without government mandates. Mathematical models were developed to explore incidence as well as variation and synchronicity in the estimated transmission rates across all 47 prefectures in Japan. An age structured model was used to explore the impact of heterogeneity in contact patterns, vaccination, and demography, specifically focusing on Okinawa, the southernmost and westernmost prefecture of Japan, due to its unique epidemiological situation compared to other prefectures. This PhD research spans the entire process, from designing and implementing social contact surveys to developing a mathematical model depicting COVID-19 dynamics in Japan. It underscores the critical role of social contacts in infectious disease transmission and highlights how cultural and country-specific factors influence human behavior during a pandemic.