In order to study the effect of organic fertilizer application on soil preferential flow characteristics of apple orchard in plateau gully region, field dyeing tracer, morphology and statistical methods were used to quantitative study the vertical dyeing soil profiles in an apple orchard in Yongshou County, Xianyang City of Shaanxi Province, the mean square error decision and preferential flow characteristic indexes were used to analyze the preferential flow characteristics in apple orchard soils under four organic fertilizer fertilization rates (0, CK; 6 000 kg/hm², T1; 9 000 kg/hm², T2; 1 2000 kg/hm², T3). The results showed that: 1) The change of soil dyeing area ratio with soil depth of all soil profiles was well fitted to the logistic curve, and the determination coefficient R² was greater than 0.986. 2) The results of matrix infiltration depth, preferential flow fraction, coefficient of variation and fractal dimension in the selected preferential flow characteristic indexes were consistent with those calculated by mean square deviation decision method, the development degree of preferential flow was T3 > T2 > T1 > CK. However, the average maximum infiltration depth, the ratio of dyeing area to preferential flow zone and the length index showed some deviations in the assessment of preferential flow degree, which was shown as T3 > T2 > CK > T1. 3) The preferential flow index obtained by mean square error decision method was 0.75 for T3, 0.59 for T2, 0.27 for T1 and 0.25 for CK, indicating the preferential flow degree is increased with the increase of fertilizer application rate. The study can provide a reference for a comprehensive evaluation of soil preferential flow characteristics and provide a basis for reasonable fertilization for orchards in plateau gully region.