In this paper, a new hybrid Manta Ray Foraging Optimization (MRFO) with Cuckoo Search (CS) algorithm (AMRFOCS) is proposed. Firstly, quantum bit Bloch spherical coordinate coding is used for the initialization of the population, which improves the diversity of the expansion of the traversal ability of the search space. Secondly, the dynamic disturbance factor is introduced to balance the exploratory and exploitative search ability of the algorithm. Finally, the unique nesting strategy of the cuckoo and Levy flight is introduced to enhance the search ability. AMRFOCS is tested on CEC2017 and CEC2020 benchmark functions, which is also compared and tested by using different dimensions and other state-of-the-art metaheuristic algorithms. Experimental results reveal that the AMRFOCS algorithm has a superior convergence rate and optimization precision. At the same time, the nonparametric Wilcoxon signed-rank test and Friedman test show that the AMRFOCS has good stability and superiority. In addition, the proposed AMRFOCS is applied to the three-dimensional WSN coverage problem. Compared with the other four 3D deployment methods optimized by metaheuristic algorithms, the AMRFOCS effectively reduces the redundancy of sensor nodes, possesses a faster convergence speed and higher coverage and then provides a more effective and practical deployment scheme.