One method for crocheting three-dimensional flowers is to stack single flowers and stitch them together. Another method is to crochet chain petals in two layers on the same flower.
According to About.com, the simplest method for creating three-dimensional crochet flowers is to crochet multiple single-layer flowers of different sizes and stack them on top of each other. For instance, start with a chain and use a slip stitch to create a ring out of the chain. Crochet a row of single stitches all around the ring, finishing with a slip stitch before moving on to the second row.
For the second row, crochet two single stitches in each single crochet from the first row, slip stitching at the end. Create petals by alternating two single stitches with a slip stitch. Make another flower slightly smaller by omitting the second row. Make another flower larger by replacing the second row of single stitches with double stitches. Stack the three flowers together, and use a tapestry needle to stitch the three flowers together.
Another way to make a three-dimensional crochet flower is to work the chain and first row as above. Next, chain eight, and secure the chain to the first single crochet. Repeat all the way around the flower. Next, slip stitch all across the perimeter of the flower.
To make the flower three-dimensional, slip stitch in the original single crochet. Chain four, and use a slip stitch to secure it to the next single crochet over. Repeat this process until there is a smaller flower inside the larger flower.