A study on transmission laser bonding of silicon and glass by Nd:YAG pulse laser is conducted. Independent and interactive effects of process parameters (power, speed and stand-off distance) on geometric elements of melt pool (melt pool depth, width, and depth/width ratio) are discussed. Based on this, effects of laser energy density on melt pool shaping for transmission laser bonding of silicon and glass are analyzed. And the relationships between energy density and geometric elements of melt pool are quantified. The matching curve of the melt pool depth/width ratio and lap-shear strength is obtained. The results indicate that the melt pool depth/width ratio stays steady when the laser energy density is more than 8 J/mm2, and lap-shear strength achieves the maximum value when the melt pool depth/width ratio is 0.25. Effects of laser energy density on melt pool shaping and bonding quality are significant.