As a widely used evaluation method, index of biotic integrity (IBI) has been used in various water bodies to evaluate the state of aquatic organisms. However, some defects and limitations in the IBI method need to be studied and solved, such as the generation and interference of deviation in IBI assessment (based on the reference site method) for time-scale trend evaluation. In this study, Songhua River Basin was used to quantitatively analyze the deviation of IBI (based on reference site method) for time-scale trend evaluation, with the survey data of macrobenthos and evaluation results of IBI during 2012-2015. In addition, the method to correct the IBI results using correction coefficients r (r: during the course of metrics scoring, the multiples of metrics base value in comparative years to initial year) and data of initial year was proposed in this work. The results showed that the value of the positive metrics (decreasing response to increasing disturbance) of reference group from 2013 to 2015 were higher than those in the initial year (2012), while the reverse metrics (increasing response to increasing disturbance) of damaged group were lower. Meanwhile, r of positive metrics was mainly ranged from 1.1 to 4.9, while 0.7 to 0.8 for the reverse metrics. The metrics 95^th of the reference group and the damaged group significantly changed in these years, with significant score deviation during the course of metrics scoring. Furthermore, during the course of evaluation criteria classification, the difference of the proportion of the worst and the best regions was 10.0%-13.4%, the disturbance from deviation was also significant on trend analysis. The comparative analysis of IBI results showed that after calibration in each year from 2012 to 2015, the proportion of excellent and good areas was higher (4.3%-13.3%) than that before calibration, while the proportion of poor areas was lower (6.7%-30.0%) than that before calibration. The results after calibration were consistent with the changes of characteristic parameters of aquatic organisms; however, the non-calibration results showed some contradiction. In summary, the deviations from the key parts during IBI assessment can significantly affect the trend analysis and determination, the deviation interference in temporal trend analysis can be preliminarily solved by the correction method.