A negative-to-positive transition of the temperature coefficients of thermal conductivity was found in the two-dimensional organic-inorganic layered complex (C4 H9 NH3 )2 CuCl4 (C4CuCl4) over the three structural phase transitions in the range 176-218 K. The coefficients of the low-temperature phases (85-200 K, α and β phases) were negative, as is typical for insulating crystals, whereas those of the high-temperature phases (200-300 K, γ and δ phases) were positive, as is typical for glasses and liquids. Single-crystal X-ray structure analyses revealed that the tilted C4 H9 NH3 + chains in the α and β phases were fully outstretched in the δ phase, and the interlayer distances between the CuCl4 2- planes increased significantly. The γ phase was an intermediate phase that crystallized with an incommensurate structure, in which the CuCl4 2- sheets formed wave-like structures consisting of connected alternating regions of β-like and δ-like moieties. In the γ and δ phases, thermal fluctuations of the C4 H9 NH3 + chains were found in the electron density maps; however, powder X-ray diffraction (PXRD) data indicated that the thermal expansion of the C4 H9 NH3 + layers was restricted by the rigid CuCl4 2- layers. This situation was considered to induce glass-like thermal conducting properties in the material, such as a positive temperature coefficient. The mean free path of the phonons estimated by using the thermal conductivities and heat capacities was a function of T-1 in the range 85-200 K, as would be expected for crystals, whereas it was approximately constant in the range 200-300 K, which is typical of glasses. In addition, the existence of soft vibration modes in the two-dimensional perovskite CuCl4 2- sheets was revealed by analysis of the incommensurate crystal structure of the γ phase. These low-energy vibration modes were believed to induce the cooperative phase transitions, along with the thermal fluctuations and van der Waals interactions in the C4 H9 NH3 + layers.