There are usually some defects and deviations in the manufacturing and installation of glulam glued-in rods joints, and there is currently no standard to follow for the design and construction of joints. Therefore, this paper focuses on the influence of installation deviation including manufacturing defects on the flexural capacity of such joints, aiming to clarify the allowable range of installation deviation. Based on the theoretical calculation method to check the beam end flexural bearing capacity of the designed joints, firstly, the finite element analysis of the joints with and without installation deviation was carried out, then the finite element analysis of the joints with installation deviation was compared with the experimental results, and the limit value of installation deviation was determined by using the finite element analysis method considering the cracking of rubber layer. The results show that: the beam end flexural bearing capacity of joints with installation deviations has decreased; the failure modes of the specimens in the test are mainly the yield of the implanted steel bars, the damage of the wood around the reinforcement holes and the cracking of the wood columns along the grain direction. If the installation deviation and adhesive cracking can be reflected in the finite element analysis, the analysis results are in good agreement with the test results. When the installation deviation is controlled within 10~25 mm, the flexural bearing capacity of the joint model is reduced by less than 5% compared to the joint model with the usual reserved gap of 10 mm.