The key factor for underwater petroleum pipeline flange connection tool is its 20 bolts synchronous lead-in nuts. The alignment accuracy of bolts and nuts is critical for bolts lead-in nuts. In order to analyze the accuracy and design issues of the pipeline flange connection tool, the robot kinematics modeling method is adopted. Using the multi-body kinematics theory to homogeneous transformation matrix, the error model of deepwater pipe flange connection tool is established through total differential of the machinery pose transformation matrix. The error model of the tool is established by computer simulation, and the effect of the structure parameters on the bolt end pose error is analyzed. Based on the method of error matching design, the error in the deepwater pipe flange automatic connection tool is determined. Considering the specific structure of the connection tool, the adjusting mechanism for bolt angle error is also designed. Therefore, the hardware compensation of bolt angle error is achieved successfully, and it improves the positioning accuracy of the bolt end. Tests on bolt lead-in prototype are conducted. The experimental results show that the bolt could successfully lead into the nut and confirm the accuracies of the error model and design of the pipeline flange connection tool.