Natural disasters, such as earthquakes, windstorms, and tsunamis, can occur all over the world, and disasters caused by human factors, such as civil wars, are also a source of major disturbance. The temporary rehousing of the population is a major problem when disasters occur. The installation of the combination house is time consuming, and tents cannot be used in the event of strong rain and wind; therefore, the container house is the most effective way of solving the rehousing problem. Natural ventilation is the main factor affecting the indoor air quality, thermal comfort, and health inside a container house, and solar radiation heat can also affect temperature changes inside. The air flow field inside a dwelling is very complex, and its flow mode is affected by inlet wind speed, inlet temperature, solar radiation heat, and the size of doors and windows, etc. In this paper, the influence of natural ventilation on the ventilation inside container houses is analyzed. Assuming that there is complex fluid motion in the activity space of the container house, it is not easy to use conventional methods to predict the flow rate. Based on the correlation analysis motion between the corresponding internal flow rates, the calculation and application method of flow is simplified from the results of the wind speed coefficient obtained previously. In addition, an analysis of flow characteristics in the container house is made; simulation analysis in the container house is made by carrying out the numerical analysis of several factors, including velocity field and temperature field. The variation state of the temperature of the environment and a numerical variation of the three-dimensional space are obtained by numerical calculation; the standard k-ε turbulence model is adopted to describe the turbulence phenomena of the fluid, and the mathematical model matched by B-spline surface is used for data analysis through the surface algorithm in order to deal with complex simulation data. The research results show that, regarding the influence of natural ventilation on container houses, the ideal relative position of openings includes the combination of asymmetric windows, followed by the central positioning of the door. The four-opening configurations, where better natural ventilation performance can be achieved, are located at different diagonal positions. The average flow velocity vector form, velocity amplitude, radiation temperature distribution, and the effect of the air volume coefficient of temperature change are analyzed. The research results show that the design of container houses can meet the requirements of air flow, such as the energy consumed by the thermal comfort space. Measurements taken over time and algorithms can also check the residents’ indoor natural ventilation and provide health care by the use of various sensors.