Background: Surface treatment of the intaglio surface of zirconia is important for bonding. However, it could affect the strength of the materials. The purpose of this study is to compare the effect of laser, etching, and air abrasion surface treatment methods to a control group on the flexural strength of three zirconia materials with two different thicknesses. (1) Methods: A total of 120 disks were divided into three groups according to the type of zirconia and the ceramic thickness. Then, according to the surface treatment method, the groups were divided into four subdivisions. The change in the microstructure of the ceramic material was investigated through Scanning Electron Microscope (EVO LS10, Carl Zeiss SMT Ltd. Oberkochen, Germany). Phase identification was performed using an X-ray diffraction device (XRD; Ultimate IV X-ray Diffractometer, Rigaku Inc., Tokyo, Japan). The flexural strength was assessed with a biaxial flexural strength test in a universal testing machine. Data were analyzed using SPSS Software (SPSS version 26.0.Armonk, NY: IBM Corp). A three-way ANOVA and a post hoc Dunnett T3 test were employed to evaluate the effect of the yttria concentration, thickness, and surface treatment on the flexural strength of zirconia (α = 0.05). (2) Results: At 0.8 mm thickness, air abrasion significantly increased the flexural strength of 3Y-TZP (1130.6 ± 171.3 MPa) and 4Y-TZP (872 ± 108.6 MPa). However, air abrasion significantly decreased the flexural strength of 5Y-TZP materials (373 ± 46.8 MPa). Laser irradiation significantly decreased the flexural strength of 5Y-TZP (347 ± 50.3 MPa), while etching significantly decreased the flexural strength of both 3Y-TZP (530 ± 48.8) and 4Y-TZP (457.1 ± 57.3). When the thickness increased to 1 mm, air abrasion continued to significantly decrease the flexural strength of 5Y-TZP materials. (3) Conclusions: There was a negative effect of surface treatment on the flexural strength at 0.8 mm thickness rather than at 1 mm thickness. Air abrasion enhances the flexural strength of 3Y-TZP and 4Y-TZP materials but significantly reduces the flexural strength of 5Y-TZP materials. Zircos-E etching and Er:YAG surface treatment methods did not significantly reduce the flexural strength of 5Y-TZP materials at 1 mm thickness and can be recommended as an alternative surface treatment for 5Y-TZP materials.