An atomic-scale finite element method was applied to analyze the sensitivities of α-, β-, γ-, and 6,6,12-graphyne-based resonators in mass detection under different boundary conditions. These sensitivities are then compared with that of a graphene-based resonator obtained in a previous study. According to the analysis results, among the graphyne-based resonators, the α type shows the highest sensitivity, while the γ type shows the lowest. In addition, the sensitivity decreases as the resonator size increases. We also find that the location of the attached mass has a significant effect on the sensitivity of the γ-graphyne-based resonators with different attached masses. The α-graphyne-based resonator with a small attached mass is also sensitive to change in location. However, the situation is different for a large attached mass. This study is significant for the future design and application of a graphynebased resonator with high sensitivity.