The invention provides an intelligent sampling and detecting system with fault accommodation function. The system comprises following steps: a. a continuous linear time invariant system model comprising actuator faults and disturbance is constructed; b. an adaptive fault diagnosis observer is designed according to the continuous linear time invariant system model in step a and an error equation is constructed; c. fault and status estimation information is obtained by use of the adaptive fault diagnosis observer in step b, and according to the fault and status estimation information, an optimal output status feedback fault-tolerant controller is further designed according to the fault and status estimation information; d. non-uniform sampling data fault-tolerant control rate is designed, and a minimum sampling interval of the non-uniform sampling data is determined; e. by use of the intelligent sampling system, sampling time is obtained, the status index is guaranteed stable even if inputting in a fault system. By use of the system, accurate and timely estimation of fixed value fault can be realized, and system stability is guaranteed by use of as little sampling output as possible.