The economic loss evaluation of disaster is the basis for disaster prevention and disaster emergency management and thus needs to be solved urgently. Computable general equilibrium (CGE) model and input-output (IO) model are the major disaster assessment methods, each of which has its own strengths and weaknesses currently. However, few comparative researches have been conducted on the economic losses of one disaster evaluated by CGE Model and IO Model based on the same disaster impact. Therefore, this paper first constructs multi-sectoral CGE model and IO model, which are commonly used in disaster loss assessment. Then, taking the Beijing “7.21 Rainstorm” in 2012 as an example, the direct losses of agricultural and transportation sectors are introduced to the basic model. After that, the economic loss ratio and comprehensive losses based on the two models can be obtained. Finally, by comparing the assessment results, the main conclusions of the evaluation mechanism are summarized. The results showed that: (1) The CGE model has a greater spillover effect upon sectors and a wider distribution of disaster-affected sectors than the IO model; (2) the range of economic loss determined by the assessment results of the CGE model and the IO model is [67.9396, 74.2739] (100 million yuan); (3) agricultural, transportation, and mining sectors are high-sensitivity sectors to rainstorm disasters. Through the comparison of the two models, the accurate economic loss of disaster can be obtained, according to which governments can take targeted measures for the prevention and early warning of disasters.