The Monte Carlo code JMCT can simulate neutron/photon/electron/proton/molecule/light radiation/atmosphere transport problems in any complicated geometry system. It supports the multi-level parallelization in scale of over one hundred thousand cores. At present, JMCT has been widely applied in radiation shielding, critical safety analysis of reactor, nuclear detection and nuclear medicine etc. JMCT3.0 is a large-scale, high-fidelity, three-dimensional general multi-particle transport Monte Carlo (MC) program, and thirteen new functions and eight new algorithms have been developed based on JMCT2.0. The computing efficiency is enhanced 30%-600% by optimizing of JCOGIN infrastructure. This paper introduces the methods and new functions of proton, low-energy photon/ electron/molecule transport in JMCT3.0. The validity of algorithms has been proved by benchmarks. The new functions are mainly used for simulations of image diagnosis, flash radiography, light radiation and atmosphere transport.