Surface plasmon resonance (SPR) biosensor based on phase detection possesses high sensitivity. Fully understanding the relations among the parameters and the phase detection is instructive for the optimal design. A five-layer mathematical model of an SPR biosensor based on phase detection is presented. We systematically analyzed the effects of the gold film, the linker and the sample on the phase detection by numerical simulation with Matlab. The numerical results show that the phase detection has the obvious selectivity, which narrows the linear detection scope. For the perfect detection resolution, gold film thickness should be from 30 to 45nm, the linker layer should be 1nm and the sample thickness should be greater than 20nm. At the same time, we compared the phase detection with the angular interrogation and found that they have the similar correlation factor, but the difference in resolution can be one order.