This Study attempts to discover the characteristics of technology and to analyze the efficiencies of resource utilization for major types of polyculture aquafarming in Taiwan. According to its jointness in production, a multiple product-multiple input translog cost function model is developed as the analytical framework. It is then implemented separately on milkfish, grass shrimp and clam, the three major species of ployculture. Empirical results show that there are net substitution relationships among inputs of all the polyculture types been investigated. However, most of the cross substitution effects are inelastic which implies that the technologies of polyculture are not fixed proportional, although their degree of production adjustments are quite low. Both the milkfish and grass shrimp polycultures can be categorized as productions of increasing returns to scale, while the technology of clam polyculture is near constant returns to scale. All subtypes of milkfish polyculture except with sand shrimps satisfied the conditions of cost complementarity. Due to its superiority in resource allocation efficiency, milkfish polyculture should be extended in the future. Production costs of grass shrimp were high relative to other aquatic products and none of the subtypes of grass shrimp polyculture satisfied the properties of joint production. Thus, the reason of choosing polyculture for grass shrimps should not be in pursuing the cost advantage but in diversifing production risks. It is not necessary to develop grass shrimp polyculture further if its stocking rate can be improved effectively. Finally, there is no consistent conclusion found about the advantage of clam polyculture.