In the detection of small size mass loading, such as a single cell, a micro droplet or an aerosol particle, the sensors with longitudinally coupled surface acoustic wave resonator (LC-SAWR) structure can hardly avoid waveform distortions. The relative size of mass loading to the sensitive surface of the detector is the main factor affecting the response of LC-SAWR. The smaller the relative size, the worse the waveform distortion. In order to avoid influences from the mass loading’s size, in this paper, a transversely coupled SAW resonator (TC-SAWR) was proposed in order to achieve high performance in sensing small size mass loadings. For the design and simulation of TC-SAWR, the two-dimensional coupling of model (2D-COM) theory and finite element method (FEM) were used in this work. In the experiment, SiO2 was deposited on the sensor’s surface as a small size mass loading. The results from simulation and experiment mutually demonstrated the advantage of TC-SAWR to conquer waveform distortion in the detection of small size mass loading.