Manipulating spectral structure often leads to degradation of speech quality, which is mainly due to insufficient smoothness of the modified spectra between frames, and ineffective spectral modification. This paper presents a new spectral modification method to improve the quality of modified speech. If frames are processed independently, discontinuous features may be generated. Therefore, a speech analysis technique called temporal decomposition (TD), which decomposes speech into event targets and event functions, is used to model the spectral evolution effectively. Instead of modifying the speech spectra frame by frame, we only need to modify event targets and event functions. This feature leads to easy modification of the speech spectra, and the smoothness of modified speech is ensured by the shape of event functions. To improve spectral modification, we explore Gaussian mixture model parameters (spectral-GMM parameters) to model the spectral envelope of each event target, and develop a new algorithm for modifying spectral-GMM parameters in accordance with formant scaling factors. We first evaluate the effectiveness of our proposed method in spectra modeling, and then apply it to two areas which require different amounts of spectral modification, emotional speech synthesis and voice gender conversion. Experimental results show that the effectiveness of our proposed method is verified for spectra modeling and spectral modification.