Here we revealed that lasers with lower repetition rates (5 kHz and 50 kHz) from an amplifier were more efficient in SHG imaging than a laser with high repetition rate (80 MHz) from an oscillator, demonstrating that peak power played a more important role than the repetition rate for high SHG yield. Although lasers with relatively high peak power damaged the cancer cells used in the imaging at a relatively lower laser power, better signal/noise ratio was achieved before the occurrence of the adverse damage. It was also revealed that photobleaching was avoided with the lower repetition rate lasers. Furthermore, the three lasers were applied in analyzing the scattered SHG intensity from colloidal BaTiO3 nanoparticles using photon counting method. All tests with the three lasers reached satisfactory results. Importantly, the lasers with low repetition rates showed great potential in the detection of weak nonlinear scattering.