Efficient nonlinear signal generation in multiphoton microscopy must be balanced against the risk of thermal damage to biological tissues. Here, we explore the maximum temperature increase in ex vivo mouse lung thin sections induced by a single two-dimensional scan using short-wave infrared (SWIR) femtosecond-pulsed lasers. We compare a conventional high repetition rate (80 MHz InSight-X3) laser with a low repetition rate (1 MHz CRONUS-3P) laser, which generates higher peak intensities, and find that at the same wavelength (1300 nm), the 1 MHz regime achieves comparable second harmonic generation (SHG) with significantly less heat accumulation, while generating twice the intensity for third harmonic generation (THG) at the same power. These results highlight the potential of low repetition rate femtosecond-pulsed laser scanning to potentially minimize heat-related photodamage, suggesting a path forward for safer and more effective deep tissue imaging in biomedical applications.