Shellfish cultivation is a sustainable method of providing human food and can help remove large amounts of CO2 from the atmosphere. Over the last two decades, longline-based structures have dominated farming systems. So far, the innovative technologies for open-ocean shellfish farming remain stagnant and need to be developed. As such, this paper preliminarily studies the operation and survivability abilities of an innovative shellfish farm under extreme wave conditions. To that end, an efficient numerical scheme with a robust implicit finite element method is established. First, the numerical modeling of a single module of the shellfish farm is conducted and the numerical results are verified against physical model tests. Then, the numerical modeling is implemented in a full-scale shellfish farm containing nine floating rafts with suspended lantern nets in a 3×3 configuration exposed to extreme wave conditions. Different angles of wave attack and shellfish rafts with and without lantern nets are fully considered, allowing an assessment of the operation and survivability abilities of the shellfish farm under extreme wave conditions in various situations. The results highlight that the angle of wave attack significantly affected the energy absorption of the mooring system. Moreover, non-linear instability such as subharmonics, which existed in the motion dynamics, can be manipulated to avoid resonant motions. This study provides insights into the evaluation of the safety design of a shellfish farm at both operational and survivability levels. The numerical method can also model other advanced offshore marine structures with multi-modules, such as floating bridges, airports, and even floating energy islands.