In this Paper, we Propose an Alignment Method for Lift-Off on Shallow Grooves in Transparent Substrates without an Extra Mask. An Assistant Metal Layer Was Deposited on the Glass Substrate with Grooves to Increase the Reflectance, and then a Layer of Photoresist for Lift-Off Process Was Coated and Patterned Aligning with the Shallow Grooves. We Compared the Effect of Aluminum and Chromium Films with Different Thickness as Reflecting Layers. an Aluminum or Chromium Film with the Thickness Larger than 10nm Provides High Enough Image Contrast of Profile of the Alignment Marks Beneath the Photoresist. the Image Contrast of Contour Profile of the Marks Was Enhanced as the Thickness Increased. Lift-Off Process Was then Implemented on the Assistant Reflecting Layer. With a 20nm Cr Layer, we Successfully Did Lithography and Finished the Lift-Off Process to Pattern a Cr/Au Layer on Shallow Grooves in a Glass Wafer. Finally, the Assistant Cr Layer Was Removed Using Dry Etching. the Assistant Metal Layer Has No Undesirable Influence on the Following Process and the Device Property.