Well deviation is a prevalent problem in deep oil and gas exploration, leading to a significant increase in drilling costs. The conventional bottom-hole assembly (BHA) anti-deviation design method does not consider the impact of the BHA structure on lateral vibration. This paper proposes an integrated BHA design method that takes into account both anti-deviation and vibration reduction. This method evaluates the BHA’s anti-deviation ability using the drilling trend angle. A negative value of the drilling trend angle indicates that the BHA can correct well deviation. A finite element linearized dynamics method is used to evaluate the lateral vibration intensity of the BHA. This method involves calculating the bending displacement caused by mass imbalance and then determining the magnitude of the bending strain energy based on this displacement. The structural factors affecting the anti-deviation ability and potential lateral vibration intensity of pendulum BHAs and bent-housing mud motor (BHMM) BHAs were studied, and field tests were conducted for verification. The research shows that for pendulum BHAs, the factor that has the greatest impact on anti-deviation ability and vibration intensity is the distance from the stabilizer to the drill bit. For BHMM BHAs, the length of the short drill collar has a significant impact on the vibration intensity. Compared with current design methods, the mechanical specific energy (MSE) of the single stabilizer pendulum BHA decreased by 12%, while the MSE of the BHMM BHA decreased by 26.4%. Both decreases indicate a reduction in vibration intensity. This study will help to further increase drilling speed while preventing well deviation.