A matrix partitioning method is proposed for the 2-D motion analysis of floating bodies. For the numerical solution, the boundary of a floating body is approximated with a series of line segments and the governing integral equation is transformed into a system of linear equations. A new solution procedure of resulting linear equation with complex coefficients is formulated and programmed using a matrix partitioning scheme and the Choleski decomposition. From the case study, it is found that the proposed method is efficient in the motion analysis of floating bodies, especially in the calculation of hydrodynamic coefficients. Also, it requires smaller memory size and less computing time compared with conventional methods.