Abstract In order to satisfy the ever-growing demand for high-performance processors for neural networks, the state-of-the-art processing units tend to use application-oriented circuits to replace Processing Engine (PE) on the GPU under circumstances where low-power solutions are required. The applicationoriented PE is fully optimized in terms of the circuit architecture and eliminates incorrect data dependency and instructional redundancy. In this paper, we propose a novel encoding approach on a sparse neural network after pruning. We partition the weight matrix into numerous blocks and use a low-rank binary map to represent the validation of these blocks. Furthermore, the elements in each nonzero block are also encoded into two submatrices: one is the binary stream discriminating the zero/nonzero position, while the other is the pure nonzero elements stored in the FIFO. In the experimental part, we implement a well pre-trained sparse neural network on the Xilinx FPGA VC707. Experimental results show that our algorithm outperforms the other benchmarks. Our approach has successfully optimized the throughput and the energy ef- ficiency to deal with a single frame. Accordingly, we contend that Nested Bitmask Neural Network (NBNN), is an efficient neural network structure with only minor accuracy loss on the SoC system