Soil CO2 flux is an important component in the study of carbon sequestration for an ecosystem, but the environmental (soil moisture, rain event, temperature etc.) and biological (photosynthesis, LAI etc.) factors that contribute to soil CO2 flux are poorly understood. This limits our ability to understand the carbon budget at the ecosystem level making it difficult to predict the impact of climate change. Two important reasons for this poor understanding have been the difficulty in making accurate soil CO2 flux measurements and the lack of continuous and long-term soil CO2 flux data at sufficiently fine temporal and spatial scales. To meet these needs, we have developed a new automated multiplexing system for obtaining reliable soil CO2 flux data at high spatial and temporal resolution. The system has the capability to continuously measure the soil CO2 flux at up to 16 locations in the field. Soil CO2 flux is driven primarily by the CO2 diffusion gradient across the soil surface. Ideally, the flux measurement should be made without affecting the diffusion gradient and without having any chamber-induced pressure perturbation. In a closed-chamber system the slope of dCO2/dt is required to compute the flux. To obtain the slope of dCO2/dt, the chamber CO2 concentration must be allowed to rise. Consequently, soil CO2 flux will be affected because of the decreased CO2 diffusion gradient inside the chamber. To minimize the impact of decreased CO2 diffusion gradient on CO2 flux measurement, the chamber CO2 concentration versus time is fitted with an exponential function. Then, soil CO2 flux is estimated by calculating the initial slope from the exponential function at time zero when the chamber touches the soil, and that is when the chamber CO2 concentration equals the ambient. Our results show that the flux estimated from a linear function, the widely used method, could underestimate CO2 flux by more than 10% as compared with that from the exponential function. An improperly designed chamber may have the problem of chamber-induced pressure perturbation during the measurement under windy conditions, due to the Venturi effect. This could lead to a high overestimation of the flux. We present a newly vented chamber design capable of maintaining pressure equilibrium between the inside and outside of the chamber under both calm and windy conditions. Field data demonstrate that our new vent design can effectively maintain the chamber pressure equilibrium under both calm and windy conditions, so that the measured flux rate represents waht occurs outside the chamber. Lastly, we will present: (1) the spatial variability of CO2 flux from a corn field near Mead, Nebraska, (2) an underestimation of soil CO2 flux when using a linear regression fit, (3) a high sensitivity of soil CO2 flux to changes in both soil CO2 concentration and chamber CO2 concentration, and (4) the capability of maintaining pressure equilibrium between inside and outside of the chamber with our new vent design.