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pH value is an important and frequently measured property in agriculture. Compared with laboratory analysis, direct soil measurement (DSM) involving the direct insertion of a pH sensor into soil, which is rapid, efficient, and inexpensive. pH value detection using DSM in soilless culture substrates exhibits a significant measuring error of 0.8 to 1.1 and is seriously affected by the component of the substrate. A super-hydrophilic pH sensor was developed with the porous TiO2 film sensitive electrode and the Ag/AgCl reference electrode. Substrates mixed by peat and vermiculite with different ratios and different mass water contents (MWC) were prepared to examine the effects on pH value detection by the super-hydrophilic pH sensors in soilless culture substrates. Statistical analysis of the measured pH values demonstrated that the errors of the super-hydrophilic pH sensors were highly and negatively correlated with MWC but showed limited influence on component ratio of the substrates. Maximum measuring error of the super-hydrophilic pH sensor was 0.81 and the measuring error discrepancy caused by the changes in component ratio was 0.23. Furthermore, a compensation model for the pH sensor was established and evaluated. The compensation results indicated that the maximum error with the super-hydrophilic pH sensor was decreased from 0.48 unit to 0.22 unit and the measuring error discrepancy caused by the changes in component ratio was decreased to 0.09. The application in soilless culture substrates picked from greenhouse showed that the measuring error of the proposed pH sensor was no more than 0.32 and decreased to 0.18 after adjusted by the compensation model. The research result revealed the influences of MWC and component ratio of soilless culture substrates on pH value detection by using super-hydrophilic pH sensors, which was helpful in improving the accuracy of DSM and can contribute to rapid and efficient pH value measurements in soilless culture substrate.