The present study proposes a low-energy consumption multipoint sampler carried by a deep-sea landing vehicle (DSLV) to meet the requirements of time series sampling in local areas and location series sampling in wide areas, and an optimization method of sampling structure based on least-squares support-vector machine (LSSVM) surrogate model and a multi-objective particle swarm optimization (MOPSO) algorithm. First, the overall structure and core components, such as the multipoint sampler’s sampling structure, were designed. The optimization variables were the cone angle, sampling tube inner diameter, and sampling tube inner hole length, which were determined by considering the force with which the sampling structure penetrates the seafloor sediment. Then, the sampling process was simulated by the finite element method-smoothed particle hydrodynamics (FEM-SPH) method, while the accurate LSSVM model of force required for sampling and sampling tube volume was established. Finally, the MOPSO algorithm was used for multi-objective optimization of model parameters of sampling structure. The optimal model of sampling structure that can provide theoretical support for the optimal design of multipoint sampler effectively reduces energy consumption and improves sampling efficiency by force required for sampling 25.89% lower and sampling tube volume 34.81% higher than the original model.