The modeling and system analysis of networked control systems(NCSs) with stochastic delay are studied. Firstly, the structure conserving model of the NCSs with the PLC controller is built by using hierarchical timed colour Petri net(HTCPN), which combines network packet loss and disorder with the system model in a novel way. Secondly, the random delay distributions from the sensor to controller and the controller to actuator are analyzed, and the relationship between the time delay and the operation of data packets in the network is established. On this basis, the Baum-Welch algorithm is used to establish two time delay hidden Markov models(HMM) to further verify the equivalence between HTCPN model and HMM.