Minichannels with the delta winglet longitudinal vortex generators (LVGs) is commonly used in the heat exchanger. However, there are few studies on the configuration of LVGs on the opposite walls and the large aspect ratio of the channel in the existing literature. In this paper, five LVGs configurations including arrangement on the opposite walls are considered, and four channel heights (1, 2, 4 and 8 mm) are considered to achieve a wide coverage of the channel aspect ratio (0.125–1). In the Reynolds number range of 3000 to 18,000, the effects of LVGs configuration and channel height on flow and heat transfer are obtained by evaluating parameters such as friction factor, Nusselt number, thermal performance factor (TPF), field synergy and frictional entropy generation rate and analyzing the vortex structure displayed by Ω method. The results show that the LVGs configuration and channel height mainly affect the main vortex behavior downstream of LVGs, but have little effect on the vortex structure near LVGs. The Mixed configuration at H = 1 mm and the CFU1 configuration at H = 2 mm have better heat transfer enhancement performance, and their Nusselt numbers are increased by 28–35% and 27–33%, respectively, compared with smooth channels. In addition, the configuration selection aiming at high overall performance under different conditions is given.