In order to meet the demand of sustainable precision agriculture for efficient and realtime acquisition of agricultural production information, flexible pH sensors have been widely studied for their small structure, easy integration and strong mechanical performance. However, the problem of deviation between multi-layer printing in the preparation process has not been solved. Therefore, aiming at improving the accuracy of sensor preparation, the registration performance of affine transformation model was discussed based on MSER. The model verification and precision test experiments were carried out to verify the feasibility of the registration model and the accuracy that the registration can achieve. The model was applied to the preparation of the flexible pH sensor chip, and finally the feasibility of the registered flexible pH sensor chip in the online monitoring of tomato organic matrix pH was verified. The experimental results showed that the accuracy of the model can reach the minimum line width of 90μm. Above 90μm, the RMSE and MAE were not more than 140μm, MRE was 3.33%~22.22%. The minimum line spacing was 500μm. Above 500μm, the RMSE and MAE were not more than 160μm, MRE was 11.67%~24%. The sensitivity of the flexible pH sensor prepared by this registration method was -61.9mV per unit pH value, and the response range was 2.0~10.0. Compared with the standard glass pH sensor, the absolute error was less than 0.15 and the relative error was less than 4.1%. The slope of the fitting curve was 0.97 and the determination coefficient R2 was 0.99. The fitting degree and accuracy was high. In the pH monitoring test of tomato organic matrix, the measurement results of the flexible and standard pH sensors had good consistency. The absolute error of the synchronous measurement results was less than 0.09, the relative error was less than 1.5%, and the RMSE between the pH monitoring results for a continuous week was only 0.05. The registered flexible pH sensor chip showed a good agricultural application prospect because of its miniaturization and close performance to the standard pH sensor. This registration method had a certain reference value for the preparation of flexible sensors processed by multiple processes, and provided a strong preparation for the subsequent monitoring of flexible pH sensor chips in the crop growth environment.