To ensure the safety of PWR-core operation, three-dimensional whole-core transient analysis needs to be carried out for the sake of the pin-power distribution. For this purpose, this paper presents “Bamboo-Transient 2.0”, a three-dimensional pin-by-pin transient analysis program. The program adopts a fully-implicit backward method with finite difference for time variable discretization, a method of exponential function expansion nodal (EFEN) SP3 for the neutron transport calculation, and a multi-channel model for the thermal feedback calculation. In addition, Picard iteration is used to couple the neutronics with thermal-feedback, which is intended to guarantee the convergence of coupling iteration at each time step. Moreover, the program can perform parallel computing based on Message Passing Interface (MPI) for the whole-core pin-by-pin transient analysis. This developed program has been applied to two commercial PWRs, viz. AP1000 and CNP1000. Numerical results of this application demonstrate that Bamboo-Transient 2.0 can yield much more refined results than the traditional legacy coarse-mesh neutron-diffusion programs based on assembly homogenization. Its pin-wise distributions of state parameters are reliable and thus can satisfactorily meet the requirements and purpose of safety analysis.