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Strict climate goals require a rapid reduction of carbon emissions across society. It is a considerable challenge to design decarbonization pathways considering co-operation in energy and carbon emissions across multiple sectors simultaneously. In order to obtain the decarbonization pathway for the whole society, this paper establishes a long-term multi-sector low-carbon transition pathway planning model. Besides inter-sectoral energy supply and demand, this study fully considers the allocation of carbon emissions quotas among different sectors by modified-grandfathering method, which takes into account both equity and efficiency principles. The decarbonization targets of different sectors, corresponding mitigation pathways and energy consumption can be calculated. China is taken as a case study. Results show that China's total energy consumption peaks at 5 billion tces around 2030, then falls below 4 billion in 2060, with the proportion of primary electricity and other clean energy reaching over 50 percent. Besides, the realisation of carbon neutralisation in China depends heavily on the improvement of carbon capture and storage (CCS) and end-use electrification rate. Moreover, the study of different quota allocation ways shows that the increase in the contribution rate of power system mitigation leads to the reduction of the total low-carbon transition costs, which also aggravates administrative difficulties. • A multi-sector model is set up to plan the long-term low-carbon transition pathway. • Modified-grandfathering allocation method can consider multiple indicator factors. • The clean energy consumption of China accounts for about 55% in 2060. • The end-use electrification rate in China is close to 70% in 2060. • The transition pathway with lower cost increases administrative difficulties. [ABSTRACT FROM AUTHOR]