To improve the calculation performance of the advanced assembly neutronics program KYLIN-II when handling the complicated boundary condition, the current paper studied the heterogeneous parallel in the KYLIN-II program based on heterogeneous parallel technology of programmable graphics card, implemented massive thread parallel computing of resonance and transport modules, and reduced the number of atomic operations of heterogeneous parallel program by optimizing iterative strategies. In order to verify the calculation accuracy and acceleration effect of heterogeneous parallel programs, calculations were carried out for test examples such as AFA3G super assembly, hexagonal plate fuel assembly and multilayer sleeve fuel cell. The results indicate that heterogeneous parallel programs will not affect the accuracy of calculation results. The KYLIN-II program after heterogeneous parallel of a single graphics card can achieve an acceleration ratio of more than 10 times. Optimizing the iterative process can effectively reduce the calculation time. Compared with the traditional multi-core parallel mechanism based on central processing unit (CPU), heterogeneous parallel of graphics card significantly reduces the economic cost of large-scale parallel of KYLIN-II program, which can be used as the direction of further parallel optimization of KYLIN-II program. Copyright ©2021 Nuclear Power Engineering. All rights reserved.