Microlenses with multiple focal lengths play an important role in three-dimensional imaging and the real-time detection of unconfined or fluctuating targets. In this Letter, we present a novel method of fabricating lens-on-lens microstructures (LLMs) using a two-step femtosecond laser wet etching process. A 3×3 LLM array was made with a diameter of 129.0 μm. The fabricated LLM has two focal lengths, 80.4 and 188.7 μm, showing excellent two-level focusing and imaging abilities. Its size and focal length can be controlled by adjusting laser power and etching time. Its surface roughness remains about 61 nm. This simple and efficient method for large-scale production of LLMs has potential applications in diverse optical systems.