Drip irrigation and flood irrigation are major irrigation methods for maize crops in the Hetao Irrigation District, Inner Mongolia Autonomous Region, China. This research delves into the effects of these irrigation methods on carbon dioxide (CO2) exchange and crop growth in this region. The experimental site was divided into drip and flood irrigation zones. The irrigation schedules of this study aligned with the local commonly used irrigation schedule. We employed a developed chamber system to measure the diurnal CO2 exchange of maize plants during various growth stages under both drip and flood irrigation methods. From May to September in 2020 and 2021, two sets of repeated experiments were conducted. In each experiment, a total of nine measurements of CO2 exchange were performed to obtain carbon exchange data at different growth stages of maize crop. During each CO2 exchange measurement event, CO2 flux data were collected every two hours over a day-long period to capture the diurnal variations in CO2 exchange. During each CO2 exchange measurement event, the biological parameters (aboveground biomass and crop growth rate) of maize and environmental parameters (including air humidity, air temperature, precipitation, soil water content, and photosynthetically active radiation) were measured. The results indicated a V-shaped trend in net ecosystem CO2 exchange in daytime, reducing slowly at night, while the net assimilation rate (net primary productivity) exhibited a contrasting trend. Notably, compared with flood irrigation, drip irrigation demonstrated significantly higher average daily soil CO2 emission and greater average daily CO2 absorption by maize plants. Consequently, within the maize ecosystem, drip irrigation appeared more conducive to absorbing atmospheric CO2. Furthermore, drip irrigation demonstrated a faster crop growth rate and increased aboveground biomass compared with flood irrigation. A strong linear relationship existed between leaf area index and light utilization efficiency, irrespective of the irrigation method. Notably, drip irrigation displayed superior light use efficiency compared with flood irrigation. The final yield results corroborated these findings, indicating that drip irrigation yielded higher harvest index and overall yield than flood irrigation. The results of this study provide a basis for the selection of optimal irrigation methods commonly used in the Hetao Irrigation District. This research also serves as a reference for future irrigation studies that consider measurements of both carbon emissions and yield simultaneously.