A spectral oriented trees based audio coder with harmonic structure reconstruction was proposed recently. Its fine scalability, low complexity, and almost MP3 quality make it suitable for Internet applications. However, during the reconstruction process, the phase information of reconstructed coefficient is absent. This may create phase discontinuities between two adjacent frames. It is audible in listening tests and makes the objective grade degraded for many testing sources. In this paper, we presented a new inter/intra-frame phase estimation method to reduce the problem and a refined harmonic reconstruction method is also applied. The quality improvement is significant. It outperforms the previous method and its performance is closer to the popular MP3pro for many audio music sources.