In order to reduce the costs of maintaining user applications and increase their scalability and manageability, companies are increasingly implementing virtual desktop infrastructures (VDI). The most important factor in migration from traditional desktops to virtual desktops is the quality of user experience, which directly depends on thin-client protocols performance in VDIs. Performance measurement of thin-client protocols is a complex task because it involves a combined analysis of intensive resource consumption along multiple dimensions (CPU, memory, and network bandwidth) between data centers and thin-client user sites. In this paper, we create a novel method and a “VDtest” benchmarking toolkit for comparing the performance of common thin-client protocols such as RDP (Remote Desktop Protocol) and PCoIP (PC-over-IP) for resource-intensive user tasks involved in graphics-based applications, using a set of “time-based criteria” such as: task downloading time, application processing time, time of video data output to thin-client console and time for I/O operations. Through empirical data analysis relating to these criteria for JPEG-transform tasks with VDtest featuring different image sizes, we show the dominant criteria to evaluate thin-client protocol performance, and explore suitable configurations based on their influence on CPU, memory and network bandwidth resources.