A method of fabricating a bonding structure having compliant bumps includes first providing a first substrate and a second substrate. The first substrate includes first bonding pads. The second substrate is disposed on one side of the first substrate and includes second bonding pads and compliant bumps disposed thereon. The second bonding pads are opposite to the first bonding pads. Next, a non-conductive adhesive layer and ball-shaped spacers are formed between the first and the second substrates. Finally, the first substrate, the non-conductive adhesive layer, and the second substrate are compressed, such that the compliant bumps on the second bonding pads of the second substrate pass through the non-conductive adhesive layer and are electrically connected to the first bonding pads of the first substrate, respectively. The ball-shaped spacers are distributed in the non-conductive adhesive layer sandwiched between the first and the second substrates for maintaining the gap therebetween.