Neutronics calculation for nuclear reactor with high-fidelity technology can significantly reduce the uncertainties propagated from numerical approximation error and model error. However, the uncertainty of input parameters inevitably exists, especially for nuclear data. On the other hand, resonance self-shielding calculation is essential for multi-group assumption based high-fidelity neutronics calculation, which introduce the implicit effect for calculation responses. In order to fully consider the implicit effects in the process of uncertainty quantification, a generalized perturbation theory (GPT) based implicit sensitivity calculation method is proposed in this paper. Combining the explicit sensitivity coefficient, which can be quantified using classic perturbation theory, the total sensitivity coefficient of calculation responses is obtained. Then the total sensitivity and uncertainty module is established in self-developed neutron transport code with high-fidelity technology-HNET. To verify the accuracy of the sensitivity calculation methods proposed in this paper, a two-dimensional fuel pin problem is chosen to verify the sensitivity results, and the numerical results show good agreement with results calculated by a direct perturbation method. Finally, uncertainty analysis for two-dimensional fuel pin problem is performed and some general conclusions are obtained from the numerical results.