Significant change of wellbore and surrounding formation temperatures during the whole drilling process for oil and gas resources often leads by annulus fluid fluxes into formation and may pose a threat to operational security of drilling and completion process. Based on energy exchange mechanisms of wellbore and formation systems during circulation and shut-in stages under lost circulation conditions, a set of partial differential equations were developed to account for the transient heat exchange process between wellbore and formation. A finite difference method was used to solve the transient heat transfer models, which enables the wellbore and formation temperature profiles to be accurately predicted. Moreover, heat exchange generated by heat convection due to circulation losses to the rock surrounding a well was also considered in the mathematical model. The results indicated that the lost circulation zone and the casing programme had significant effects on the temperature distributions of wellbore and formation. The disturbance distance of formation temperature was influenced by circulation and shut-in stages. A comparative perfection theoretical basis for temperature distribution of wellbore-formation system in a deep well drilling was developed in presence of lost circulation.