Sampling-based algorithms, which eliminate "unimportant" computations during forward and/or backpropagation (BP), offer potential solutions to accelerate neural network training. However, since sampling introduces approximations to training, such algorithms may not consistently maintain accuracy across various tasks. In this work, we introduce a variance-controlled adaptive sampling (VCAS) method designed to minimize the computational load of BP. VCAS computes an unbiased stochastic gradient with fine-grained layerwise importance sampling in data dimension for activation gradient calculation and leverage score sampling in token dimension for weight gradient calculation. To preserve accuracy, we control the additional variance introduced by learning the sample ratio jointly with model parameters during training. We assessed VCAS on multiple fine-tuning and pre-training tasks in both vision and natural language domains. On all the tasks, VCAS can preserve the original training loss trajectory and validation accuracy with an up to 73.87% FLOPs reduction of BP and 49.58% FLOPs reduction of the whole training process.