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The sensing mechanism of InAlN/GaN high electron mobility transistors (HEMTs) is investigated systematically by numerical simulation and theoretical analysis. In detail, the influence of additional surface charge on device performance and the dependence of surface sensing properties on InAlN barrier thickness are studied. The results indicate that the saturation output drain current I_dsat and two-dimensional electron gas (2DEG) concentration increase with the increase of positive surface charge density, which decrease with the increase of negative surface charge. The influence of negative surface charge on device performance is more remarkable than that of positive surface charge. Additionally, the modulation ability of surface charge on device performance increases with the decrease ofInAlN barrier thickness. The modulation of surface charge on device performance and the influence of barrier thickness on surface sensing sensitivity are mainly attributed to the variation of the energy band structure, surface potential and 2DEG concentration in the HEMT heterostructure. This work provides important support for structural optimization design of GaN-based HEMT sensors.