The photothermal effects of laser on tissue are widely used in ophthalmology to treat retinal diseases. The accurate modelling of retinal laser surgery will prove valuable guidance for clinic treatment. There are several important issues should be carefully evaluated during retinal laser surgery modelling, including the eye geometry (whole eye or fundus only, retinal pigment epithelium layer incorporated or not), blood perfusion and natural convection. In previous publications, the existence of the anterior part of eyeball and retinal pigment epithelium layer is neglected to simply the eye geometry due to low laser light absorption (anterior part of eyeball) or small volume occupation (retinal pigment epithelium layer), respectively. However, the justification of this treatment has not been conducted. In this study, we will quantitatively investigate these factors systemically in a large pulse duration range that covers all the retinal laser surgery used in clinic. To do this, we present a bioheat transfer model for the simulation of the thermal response of the eye to laser irradiation. In the simulation, the 3D whole-eye geometry is considered. The Pennes bioheat transfer equation is adopted for the whole-eye temperature modelling. Simultaneously, we treat the fundus as a multilayered medium that all primary components, including RPE layer, are considered for first time in whole eye modelling. Our model calculates the thermal responses of the eye during laser retinal surgery with the pulse duration from nanosecond to tens of second. The effects of eye geometry, blood perfusion and natural convection are clearly clarified based on the laser pulse duration and incident energy used. The results show that neglecting the anterior part of eyeball will introduce the computational error more than 27 %. The existence of the retinal pigment epithelium layer should always be considered in retinal laser surgery modelling in all pulse durations used in clinic, otherwise more than 20 % computational error will be generated. When the pulse duration is longer than 10s, the effect of blood perfusion and natural convection in vitreous body should both be considered.