The performance of small animal PET scanners depends on the energy window (EW) and timing window (TW). In National Electrical Manufacturers Association (NEMA) Standards Publication NU 4-2008, detailed procedures of the performance measurements are defined, but the EW and TW are not specified. In this work, the effects of EW and TW on the physical and imaging performance of Shenzhen Institute of Advanced Technology small animal PET (SIAT aPET) will be evaluated. First, the flood histogram, energy resolution, and timing resolution were measured for a detector of SIAT aPET. Second, the spatial resolutions were measured with different EWs. Third, the sensitivities, the scatter fractions (SFs), and noise equivalent count rates (NECRs) of a mouse-sized phantom and a rat-sized phantom, the recovery coefficients (RCs) of rods of different sizes, and the percentage standard deviation (%STD) of the NEMA image quality phantom were measured for different EWs and TWs. Last, images of a hot rod phantom, a mouse heart, and a rat brain were acquired from the scanner with different EWs. The SIAT aPET detectors provided good flood histograms such that all but the corner crystals can be resolved even with lower energies of 250-350keV, an average energy resolution of 21.1 ± 1.9%, and an average timing resolution of 2.63 ± 0.69ns. The average spatial resolutions obtained with EWs of 250-350keV and 450-550keV are 0.68mm and 0.75mm. For EWs of 250-750keV, 350-750keV, and 450-750keV with a fixed TW of 12ns, the sensitivities at the center of field of view (FOV) are 16.0%, 11.9%, and 8.2%, the peak NECRs of a mouse-sized phantom are 355.6 kcps, 324.4 kcps, and 249.4 kcps, and the peak NECRs of a rat-sized phantom are 148.5 kcps, 144.3 kcps, and 117.7 kcps, respectively. For the TWs of 4ns, 8ns,12ns, and 20ns with a fixed EW of 350-750keV, the sensitivities at the center of FOV are 9.6%, 11.4%, 11.9%, and 12.2%, the peak NECRs of a mouse-sized phantom are 260.1 kcps, 311.5 kcps, 324.4 kcps and 324.9 kcps, and the peak NECRs of a rat-sized phantom are 110.5 kcps, 137.3 kcps, 144.3 kcps, and 142.6 kcps, respectively. Narrowing the EW and TW improves the RCs of rods of all sizes, and the %STD of images obtained with different EWs and TWs are similar. Rods with diameter down to 0.8mm can be visually resolved from images of the hot rod phantom obtained with different EWs. Images of mouse heart with high spatial resolution and rat brain with detail brain structure were obtained with different EWs. Images of both phantom and in vivo animals obtained with different EWs only showed subtle difference. The performance of SIAT aPET under different EWs and TWs was compared. The EW and TW affect the sensitivity, SF, and NECR but not the spatial resolution and animal images of SIAT aPET, which imply that careful optimization of the EW and TW is not required.