With commercialization, marine science and military applications in offshore and shallow waters is increasing, the development of the small surface vessels are getting greater, and that design targets are focus on multi-functional platforms, smart navigation and autonomous, etc. Therefore, the goals of multi-purpose small surface vessels such as the coastal patrol, offshore observation and data collection, intelligence reconnaissance, anti-mine warfare, marine shooting training targets, and so on. In currently, to achieve these missions, the length of most small surface vessels were designed less than 10 meters. Furthermore, based on these multi-propose requirements, this study will explore the configuration design of monohull and trimaran, combine the research source of the Horizontal Circulating Water Channel (HCWC), through the ship model test to acquire experimental data. In addition, to promote the study quality and experimental efficiency, we applied Taguchi design of experimental (DOE) and the variance of analysis (ANOVA) to compare the resistance and payload of various configurations ship design. In this study, we defined two control factors (such as factor-A is Longitudinal distance, factor-B is Lateral distance) and set up three-level factorial design, and planned factorial experiment based on Taguchi orthogonal array L9 (34). Also used the neural network and training metamodeling. This metamodeling was decided by relative coefficient (R) and decision coefficient (R2). According to this metamodeling, and then, applied the genetic algorithm to search the best solution such as A2B3. The results of this study showed that the resistance performance of the trimaran is better than the monohull while the volume Froude number Fr∇ > 0.95, and the optimum configuration has greater resistance performance at both higher and lower speed fields to achieve robust design. In the other hand, this paper will also discuss the feasibility and effectiveness of the installation space and multi-function performance on platform. Hence, for payload study, we also applied ANOVA to analyze these nine different configurations, and indicated a significant main effect for factor-B. However, no significant main effect for factor-A and interaction effect were found. To conclude, this study may be of importance in explaining small surface vessel design, as well as in providing ship designer with a better understanding of trade-off about speed and payload. While this study has its limitations (such as HCWC characteristic dimension), it is hoped that it could as a basis for further study in the multi-functional small surface vessel.