The rate and quality of microscale meniscus confined electrodeposition represent the key to micromanipulation based on electrochemistry and are extremely susceptible to the ambient relative humidity, electrolyte concentration, and applied voltage. To solve this problem, based on a neural network and genetic algorithm approach, this paper optimizes the process parameters of the microscale meniscus confined electrodeposition to achieve high-efficiency and -quality deposition. First, with the COMSOL Multiphysics, the influence factors of electrodeposition were analyzed and the range of high efficiency and quality electrodeposition parameters were discovered. Second, based on the back propagation (BP) neural network, the relationships between influence factors and the rate of microscale meniscus confined electrodeposition were established. Then, in order to achieve effective electrodeposition, the determined electrodeposition rate of 5 × 10−8 m/s was set as the target value, and the genetic algorithm was used to optimize each parameter. Finally, based on the optimization parameters obtained, we proceeded with simulations and experiments. The results indicate that the deposition rate maximum error is only 2.0% in experiments. The feasibility and accuracy of the method proposed in this paper were verified.