The interactions between CO2 flux, an important component of ecosystem carbon flux, and climate change vary significantly among different ecosystems. In this research, the inter-annual variation characteristics of ecosystem respiration (RE), gross ecosystem exchange (GEE), and net ecosystem exchange (NEE) were explored in the temperate grassland (TG) of Xilinhot (2004–2010), the subtropical artificial coniferous forest (SACF) of Qianyanzhou (2003–2010), and the tropical rain forest (TRF) of Xishuangbanna (2003–2010). The main factors of climate change affecting ecosystem CO2 flux were identified by redundancy analysis, and exponential models and temperature indicators were constructed to consider the relationship between climate change and CO2 flux. Every year from 2003 to 2010, RE and GEE first increased and then decreased, and NEE showed no significant change pattern. TG was a carbon source, whereas SACF and TRF were carbon sinks. The influence of air temperature on RE and GEE was greater than that of soil temperature, but the influence of soil moisture on RE and GEE was greater than that of air moisture. Compared with moisture and photosynthetically active radiation, temperature had the greatest impact on CO2 flux and the exponential model had the best fitting effect. In TG and SACF, the average temperature was the most influential factor, and in TRF, the accumulated temperature was the most influential factor. These results provide theoretical support for mitigating and managing climate change and provide references for achieving carbon neutrality.