The transition zone from the Loess Plateau to the Qinghai-Tibet Plateau is one of the regions with most dramatic changes in agricultural production mode and most sensitive response to the carbon balance effect. This paper analyzed the carbon balance of the agriculture system along the altitude gradient in Tongwei, Weiyuan and Xiahe counties. The results showed that with the increase of altitude, the carbon emission, carbon fixation and carbon sink capacity of crops per unit area decreased accordingly, while the average carbon emission, carbon fixation and carbon source capacity of each household in livestock system increased. The integrated crop-livestock production system changed from carbon sink to carbon source. The average carbon emission of each household rose with altitude, but the carbon fixation was the opposite. The change of percentage ofhousehold in the transition zone from the Loess Plateau to the Qinghai-Tibet Plateau with carbon balance could be fitted with Logistic equation. In the crop system of Tongwei, Weiyuan and Xiahe with the altitude increase, carbon emission at the inflection point where the household percentage accounted for 50.0% was 1491, 857 and 376 kg CE·household, and carbon fixation was 6187, 3872 and 778 kg CE·household, respectively. For the livestock system, carbon emission was 2218, 3725 and 49511 kg CE·household, and carbon fixation was 138, 230 and 2706 kg CE·household, respectively. For the integrated crop-livestock system, carbon emission was 3615, 4583 and 49918 kg CE·household, and carbon fixation was 6289, 4113 and 3819 kg CE·household, respectively, which could be the key point for the regulation of regional carbon balance.
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