A method for autonomous vehicle fault diagnosis and protection for an autonomous vehicle system, comprising steps of: S 1: acquiring fault information of at least one functional module in an autonomous vehicle system for an autonomous vehicle and overall state information of the autonomous vehicle system in real time; S2: determining fault handling information of the vehicle by comprehensively analyzing the acquired fault information and the overall state information of the autonomous vehicle system; and S3: sending the fault handling information to a control and execution layer of the vehicle for processing, wherein, the overall state information of the autonomous vehicle system in step S1 is system state information acquired from an inner core of the autonomous vehicle system, the fault handling information in step S2 is used for classifying faults of the at least one functional module into three fault levels including a high level, a medium level and a low level, when the fault level is determined as the high level, a lower-layer vehicle controller executes an emergency stop instruction to stop the vehicle after the control and execution layer acquires the fault handling information, when the fault level is determined as the medium level, the control and execution layer controls the vehicle to slow down after acquiring the fault handling information, wherein the at least one functional module in step S1 comprises core algorithm modules, sensor modules and a vehicle control module, the core algorithm modules comprise a perception module, a positioning module, a decision module and a control module, when the fault level is determined as the low level, the control and execution layer takes no action specific to the fault handling information after acquiring the fault handling information, and step S3 further comprises storing locally and uploading to a cloud server the fault information of the at least one functional module and the overall state information of the autonomous vehicle system. S 1: acquiring fault information of at least one functional module in an autonomous vehicle system for an autonomous vehicle and overall state information of the autonomous vehicle system in real time; S2: determining fault handling information of the vehicle by comprehensively analyzing the acquired fault information and the overall state information of the autonomous vehicle system; and S3: sending the fault handling information to a control and execution layer of the vehicle for processing, wherein, the overall state information of the autonomous vehicle system in step S1 is system state information acquired from an inner core of the autonomous vehicle system, the fault handling information in step S2 is used for classifying faults of the at least one functional module into three fault levels including a high level, a medium level and a low level, when the fault level is determined as the high level, a lower-layer vehicle controller executes an emergency stop instruction to stop the vehicle after the control and execution layer acquires the fault handling information, when the fault level is determined as the medium level, the control and execution layer controls the vehicle to slow down after acquiring the fault handling information, wherein the at least one functional module in step S1 comprises core algorithm modules, sensor modules and a vehicle control module, the core algorithm modules comprise a perception module, a positioning module, a decision module and a control module, when the fault level is determined as the low level, the control and execution layer takes no action specific to the fault handling information after acquiring the fault handling information, and step S3 further comprises storing locally and uploading to a cloud server the fault information of the at least one functional module and the overall state information of the autonomous vehicle system.