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This paper presents a source-filter based adaptive harmonic model (aHM) that can modify prosody of given speech signals. Although the conventional aHM generates a homogeneous replication of the input speech, it is not suitable for prosody modification since temporal and spectral information are interweaved. The proposed method overcomes such limitation by further decomposing the harmonic parameter extracted from aHM into source and filter related components. By applying source-filter structure to aHM, the proposed algorithm can modify pitch of the synthesized speech with introducing only minor degradation. Both objective and subjective test results show that the proposed algorithm can naturally manipulate pitch contour, of which performance is much better than conventional algorithms such as pitch synchronous overlap add (PSOLA) and speech transformation and representation using adaptive interpolation of weighted spectrum (STRAIGHT).