Abstract: Pinellia ternata lectin (PTL) is considered as the toxic substance of Pinellia ternata, and is the main cause of irritation in raw Pinellia tubers. The content of PTL decreases after processing. Pinellia tubers are processed with ginger extract, liquorice or alum to reduce the toxicity and get processed products, such as Jingbanxia, Qingbanxia and Fabanxia. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method has the advantages of low cost, rapid and automated operation, which is suitable for the detection of intact proteins. However, MALDI-TOF MS is difficult to perform quantitative analysis of intact protein due to its low sensitivity and repeatability. It is important to establish a rapid analysis method for the detection of PTL by improving the sensitivity and repeatability of MALDI-TOF MS. Cellulose nanocrystal (CNC) is one of the nano materials with rod-like structure, which has wide applications due to its large specific surface area, abundant hydroxyl groups. It has the ability to reduce protein aggregation, so can reduce the aggregated protein ion nM+H⁺ signals in MALDI-TOF MS. In this study, CNC assisted MALDI-TOF MS combined with internal standard method was used to quantitative analyze PTL during processing of Pinellia ternata. The preparation time and proportion of CNC-assisted samples were optimized, and Triticum vulgaris lectin (TVL) was used as internal standard to directly analyze PTL in processed products and their supernatant. Good repeatability of MALDI-TOF MS analysis could be successfully achieved by adding CNC to the protein sample solution. CNC-assisted MALDI sample preparation could effectively solve the quantitative analysis problem of MALDI-TOF MS, improve the sensitivity, linearity and repeatability. During the processing of raw Pinellia tubers, the PTL in raw tubers was gradually dissolved in the Pinellia tubers extract. As the processing time increased, the content of PTL in the three types of processed products gradually decreased, and gradually increased in their supernatant. The content of PTL in the soak supernatant tended to increase and then decrease due to pH change. In addition, PTL was not detected in many batches of processed products from different manufacturers. Instead, PTL was detected at high levels in raw Pinellia tubers. The method provides a scientific basis for the mechanism of Pinellia ternata processing on toxic PTL, as well as for the optimization of processing production and technological innovation.