The purpose of this study is to simulate the heat transfer problem when the 3-D Alanine tissue is heated by the gold nanoparticle in the field of molecular dynamics. In this paper, the Alanine molecule is adopted and its parameters are available in the GROMACS protein data bank. A computing algorithm is developed to evaluate the heat transfer phenomena in the nano-scale biological system based on the molecular dynamics and the protein data bank. The value of the thermal conductivity of Alanine is calculated from the autocorrelation function of the Green-Kubo formalism and this result has a roughly approximation with the bulk thermal conductivity reported by experimental data . Two kinds of problems are investigated in the paper. One is the Alanine tissue heated by the constant heat source and the other is by the time-varying heat source. The numerical results show that a temperature jump exists around the source and the temperature profiles drop to the environmental temperature within a very short distance. It concludes that only a small region around the nano-scale heat source is affected by the heated process. Therefore, the results of the nanoparticle-heated method could be applied to the clinical therapy of tumor, and the normal cells are destroyed only within a smaller region than those of chemotherapy or surgery.