Mode matching plays an important role in measuring the continuous variable entanglement. For the signal and idler twin beams generated by a pulse pumped fiber optical parametric amplifier (FOPA), the spatial mode matching is automatically achieved in single mode fiber, but the temporal mode property is complicated because it is highly sensitive to the dispersion and the gain of the FOPA. We study the temporal mode structure and derive the input-output relation for each temporal mode of signal and idler beams after decomposing the joint spectral function of twin beams with the singular-value decomposition method. We analyze the measurement of the quadrature-amplitude entanglement, and find mode matching between the multi-mode twin beams and the local oscillators of homodyne detection systems is crucial to achieve a high degree of entanglement. The results show that the noise contributed by the temporal modes nonorthogonal to local oscillator may be much larger than the vacuum noise, so the mode mis-match can not be accounted for by merely introducing an effective loss. Our study will be useful for developing a source of high quality continuous variable entanglement by using the FOPA
