Large earthquakes not only directly damage buildings but also trigger debris flows, which cause secondary damage to buildings, forming a more destructive earthquake-debris flow disaster chain. A quantitative assessment of building vulnerability is essential for damage assessment after a disaster and for pre-disaster prevention. Using mechanical analysis based on pushover, a physical vulnerability assessment model of buildings in the earthquake-debris flow disaster chain is proposed to assess the vulnerability of buildings in Beichuan County, China. Based on the specific sequence of events in the earthquake-debris flow disaster chain, the seismic vulnerability of buildings is 79%, the flow impact and burial vulnerabilities of damaged buildings to debris flow are 92% and 28% respectively, and the holistic vulnerability of buildings under the disaster chain is 57%. By comparing different vulnerability assessment methods, we observed that the physical vulnerability of buildings under the disaster chain process is not equal to the statistical summation of the vulnerabilities to independent hazards, which implies that the structural properties and vulnerability of buildings have changed during the disaster chain process. Our results provide an integrated explanation of building vulnerability, which is essential for understanding building vulnerability in earthquake-debris flow disaster chain and building vulnerability under other disaster chains.