Negative thermal expansion (NTE) is an effect of a material contracting upon heating, and NTE materials are useful for the preparation of zero thermal expansion (ZTE) composite materials for applications in energy conversion and electronic devices. In this work, the NTE behaviour of graphdiyne (GDY) was observed and studied by temperature-dependent Raman spectroscopy. The characteristic Y mode in Raman spectra of GDY film exhibit blueshift with increasing temperature, in contrast to the redshift of positive thermal expansion materials. Our theoretical calculations show that the dimension of GDY decreases when the temperature is elevated, and the blueshift of the Y mode is due to the contraction of GDY. The thermal expansion coefficient (TEC) of GDY in the temperature range of 180–420 K was found to be negative, − 7.18 × 10−6 K−1 at room temperature. Our results provide a measure of the thermal property of GDY and indicate promising applications of GDY in NTE composite materials.