In this paper, the third-order nonlinear optical properties of covalent organic framework materials with conjugated amphoteric ion structure are studied for the first time. A highly ordered crystalline ultrathin films of the ionic covalent organic framework material PySQ-iCOF was successfully fabricated using a solid-liquid interface method, meanwhile the building units extracted to be independent small molecule, 1-PySA, were synthesized for comparative studies. Compared to 1-PySA, PySQ-iCOF possesses not only a larger conjugated system but also exhibits enhanced polarization and charge transfer capabilities. The NLO properties of PySQ-iCOF and the small molecule 1-PySA were investigated using Z-scan technique at a wavelength of 532 nm. The results revealed that the PySQ-iCOF thin film exhibits outstanding NLO performance. Specifically, it demonstrates saturable absorption under nanosecond (ns) pulse laser irradiation (β = -9.59×10-6 m/W), while exhibiting reverse saturable absorption under femtosecond (fs) pulse conditions (β = 6.91×10-8 m/W). Furthermore, the PySQ-iCOF film exhibits strong negative refractive nonlinearity, -6 × 10-12 m2/W for ns and -3.8 × 10-13 m2/W for fs, respectively. Transient absorption spectroscopy studies indicate that the pulse-width-dependent nonlinear absorption characteristics of the PySQ-iCOF film originate from the generation of triplet excited states. Both the nonlinear absorption coefficient and nonlinear refractive index of the PySQ-iCOF film surpass those of most reported organic materials measured under comparable conditions, which provides huge potential in all-optical manipulating and switching at the nanoscale as outstanding nonlinear optical materials.