Laser ablation technique is a novel method for obtaining a surface with a low secondary electron yield (SEY) that can mitigate electron cloud in high-energy accelerators. Before the installation of laser processed aluminum alloy, surface cleaning is of the essence to reduce the contaminations of ultra-high vacuum systems for providing appropriate pressure for beam operation consequently. Laser processed aluminum alloy is one of the crucial candidates for the vacuum system construction of future accelerators. Moreover, ultrasonic cleaning is an essential procedure for most materials applied in vacuum systems. Therefore, in order to verify the stability of the laser created structures by ultrasonic cleaning and evaluate the impact of the cleaning on the SEYs, the surface topographies, and the surface chemistries of laser treated aluminum alloy, SEY measurements and related tests were performed. After ultrasonic cleaning, the SEYs of laser treated aluminum alloy increased from 0.99, 1.05, and 1.16 to 1.43, 1.74, and 1.38, respectively. Compared to the surface roughness of uncleaned laser treated aluminum samples, the cleaned laser treated ones decreased from 10.7, 7.5, and 14.5 to 9.4, 6.9, and 12.9, respectively. The results indicate that ultrasonic cleaning can induce the SEY increase of laser processed aluminum alloy. The correlative mechanism between the surface morphology, the surface chemistry, and SEY increase were analyzed for the first time.