The invention discloses a quantum system ground state energy estimation method and system, and relates to the technical field of quantum. According to the invention, the wave function output by the PQC is post-processed by adopting the neural network, the neural network can play a role of a general function approximator, and compared with a Jastrow factor, the neural network has higher expression ability and ground state energy approximation ability, so that improvement of the accuracy of ground state energy estimation is facilitated. Moreover, the measurement circuit is added after the PQC, the measurement circuit is used for executing the transformation processing corresponding to the Fouli character string on the output quantum state of the PQC, the transformed output quantum state is obtained, and the resource consumption in the measurement estimation process can be reduced through the transformation, so that under the consumption of polynomial resources, measurement and unbiased estimation of the Fouli character string and even the general Hamiltonian are completed.