This paper introduces a new computational efficient Dilution of Precision (DOP)-based landmark exclusion method while ensuring the safety of the LiDAR-based navigation system that uses an innovation-based Nearest-Neighbor (NN) Data Association (DA) process. The NN DA process finds a correct landmark association hypothesis among all potential landmark permutations using Kalman filter innovation vectors. This makes the computational load increases exponentially as the number of landmarks increases. In this paper, we thus exclude landmarks by introducing DOP that quantifies the geometric distribution of landmarks as a way to minimize the loss of integrity performance that can occur by reducing landmarks. The number of landmarks to be excluded is set as the maximum number that can satisfy the integrity risk requirement. For the verification of the method, we developed a simulator that can analyze integrity risk according to the landmark number and its geometric distribution. Based on the simulation, we analyzed the relationship between DOP and integrity risk of the DA process by excluding each landmark. The results showed a tendency to minimize the loss of integrity performance when excluding landmarks with poor DOP. The developed method opens the possibility of assuring the safety risk of the Lidar-based navigation system in real-time applications by reducing a substantial amount of computational load.