In the modern logistic system, the modern warehouse plays an important part in it, affording more functions than just storage. Fire disaster is one of the most common disasters in the modern warehouse, causing huge problems. It is necessary to protect the security of the modern warehouse by specific measures. This study takes a modern logistics transit warehouse as an example, and mainly discusses the fire risk probability in the different areas and the total fire disaster risk assessment using the total probability formula and Gustav civil fire risk analysis method. This study uses the actual data of the warehouse itself and some quantitative methods to calculate parameters indicating the fire risk of goods and people in the Gustav method, and puts them together for a final assessment. Results show that the main storage area have the highest risk for both facilities and stuff, even though the whole warehouse is relatively safe. Finally, this study gives out some practical suggestions for this kind of warehouse, mainly in the aspects of the completeness of fire warning system and Installation of fire-fighting facilities.