In order to solve the delay caused by different sampling frequencies of multisensors in position estimation of plant protection unmanned aerial vehicle (UAV), a variable structure linear moving horizon estimator (VSL-MHE) was designed to process delay measurement values. Firstly, the measurement data of multiple sensor was serialized. Then the linear index method was used to determine the coordinates of the zero elements in the arrangement term, and the weighting matrix in the cost function was updated with the coordinates of the zero elements to change the structure of the estimator. Finally, the plant protection UAV position was estimated by VSL-MHE. The accuracy of the position estimation was verified from the actual flight tests. In the indoor experiment, the GPS output was simulated by the output of OptiTrack motion capture system, the frequency could be controlled in the range of 2~20Hz. Through the fixedpoint hover experiment, the positions estimated from VSL-MHE, MHE and the circular iterated extended Kalman filter (CIEKF) were compared with that obtained from OptiTrack, respectively. The maximum positional offset of VSL-MHE was smaller than the positional offset of the CIEKF and MHE. In the outdoor experiment, the range of path planning was set to be 40m×30m, and the maximum positional deviation from the VSL-MHE was less than that estimated from CIEKF and MHE. The experiment results showed that VSL-MHE can effectively reduce the adverse effects on the accuracy of position estimation.