Secondary radiation force can be an attractive force causing aggregates of encapsulated microbubbles in ultrasonic molecular imaging. The influence of the secondary radiation force on aggregation between two coated bubbles is investigated in this study. Numerical calculations are performed based on four simultaneous differential equations of radial and translational motions. Results show that the secondary force can change from attraction to repulsion during approach, and stable microbubble pairs can be formed in the vicinity of resonant regions; the possibility of microbubble aggregations can be reduced by using low exciting amplitude, ultrasonic frequencies deviating from the resonant frequencies or microbubbles with small compressibility.