For the condition that composite stringer cannot connect the titanium joints properly due to the manufacturing defect, three kinds of connecting type comparison tests are designed and the test conditions are normal connection, stringer vertical edge with failure and stringer free edge with failure, respectively. FEM is used to study the changes of the failure mode and failure load of the structure under the out-of-tolerance condition. The results show that the three connection type structures have the same failure mode which fails along the 45° fiber of the skin precast crack; three different conditions almost have no influence on connection stiffness; the condition that stringer vertical edge with failure has less effect on connection strength, the failure loads decrease 5.31%; the condition that stringer free edge with failure has greater effect on connection strength, the failure loads decrease 22.13%. The condition that stringer free edge with failure is the most severe failure condition.