Graphics Processing Units (GPUs) support dynamic voltage and frequency scaling (DVFS) in order to balance computational performance and energy consumption. However, there still lacks simple and accurate performance estimation of a given GPU kernel under different frequency settings on real hardware, which is important to decide best frequency configuration for energy saving. This paper reveals a fine-grained model to estimate the execution time of GPU kernels with both core and memory frequency scaling. Over a 2.5x range of both core and memory frequencies among 12 GPU kernels, our model achieves accurate results (within 3.5%) on real hardware. Compared with the cycle-level simulators, our model only needs some simple micro-benchmark to extract a set of hardware parameters and performance counters of the kernels to produce this high accuracy.