The simulation of an ocean general circulation model for the earth simulator (OFES) is transformed to an isopycnal coordinate to investigate the spatial structure and seasonal variability of the Mindanao Undercurrent (MUC). The results show that (1) potential density surfaces, σ θ =26.5 and σ θ =27.5, can be chosen to encompass the MUC layer. Southern Pacific tropical water (SPTW), Antarctic Intermediate Water (AAIW) and high potential density water (HPDW) constitute the MUC. (2) Climatologically, the MUC exists in the form of dual-core. In some months, the dual-core structure changes to a single-core structure. (3) Choosing section at 8°N for calculating the transport of the MUC transport is reliable. Potential density constraint provides a good method for calculating the transport of the MUC. (4) The annual mean transport of the MUC is 8.34×106 m3/s and varies considerably with seasons: stronger in late spring and weaker in winter.