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The phase-modulated quadrature squeezing in the system that composed of two coupled cavities interacting with a two-level atom is investigated. The variances of the amplitude and phase quadrature of the output field are calculated. It tus out that the squeezing behaviors of the output field can be obviously modified due to the phase difference of the coupling strengths between the atom and the two cavities. The squeezing in one quadrature (i.e., phase quadrature) can be transferred into another (i.e., amplitude quadrature), or the quadrature squeezing located at the low-frequency region can be transferred into the high-frequency region by modulating the relative phase of the coupling strengths. Furthermore, the effects of the decay mismatch between the two cavities and the coupling mismatch between the atom and the cavities on the quadrature squeezing have been discussed. The results show that both the decay mismatch and the coupling mismatch play a positive role in generating better quadrature squeezing.