In this work, an optimization method for the 3D container loading problem with multiple constraints is proposed. The method consists of a genetic algorithm to generate an arrangement of cargo and a fitness evaluation using a physics simulation. The fitness function considers not only the maximization of the container density and fitness value but also several different constraints such as weight, stack-ability, fragility, and orientation of cargo pieces. We employed a container shaking simulation for the fitness evaluation to include constraint effects during loading and transportation. We verified that the proposed method successfully provides the optimal cargo arrangement for small-scale problems with about 10 pieces of cargo.