With the increasing demands of high fidelity neutronics analysis and the development of computer technology, Monte Carlo method is becoming more and more attractive in accurate simulation of pebble bed High Temperature gas-cooled Reactor (HTR), owing to its advantages of the flexible geometry modeling and the use of continuous-energy nuclear cross sections. For the double-heterogeneous geometry of pebble bed, traditional Monte Carlo codes can treat it by explicit geometry description. However, packing methods such as Random Sequential Addition (RSA) can only produce a sphere packing up to 38% volume packing fraction, while Discrete Element Method (DEM) is troublesome and also time consuming. Moreover, traditional Monte Carlo codes are difficult and inconvenient to simulate the mixed and polytype particles or pebbles. A new random geometry method was developed in Monte Carlo code RMC to simulate the particle transport in polytype particle/pebble in double heterogeneous geometry systems. This method was verified by some test cases, and applied to the full core calculations of HTR-10 benchmark. The reactivity, temperature coefficient and control rod worth of HTR-10 were compared for full core and initial core in helium and air atmosphere respectively, and the results agree well with the benchmark results and experimental results. This work would provide an efficient tool for the innovative design of pebble bed, prism HTRs and molten salt reactors with polytype particles or pebbles using Monte Carlo method.