Survivin exists as a homodimeric conformation to act as a suppressor of apoptosis in organisms. Previously, we found that the deletants with truncations of N-terminal residues up to Arg18 lost the binding ability to Smac/DIABLO but not the binding force of homodimers. In order to establish the relationship between function and structural stability, thermal unfolding of SurF and its deletants in buffer have been studied in the present paper. The fluorescent results indicated that with the removal of the N-terminus, the thermal stability of the tertiary structure dropped vigorously, especially for SurΔN18. However, using circular dichroism (CD) spectroscopy, we observed that the main unfolding of the secondary structures was not affected very much with N-terminus deletion. Fourier transform infrared (FT-IR) spectroscopy and two-dimensional (2D) correlation analysis were further used to provide structural information that occurred in the main transitions, which were associated with conformational changes of several β-components and α-helix, followed by the gain of some aggregations and random coils at high temperature. In addition, more aggregates were found to form for the longer N-terminal deletants during the main unfolding.