In this study, a method combining room temperature pulsed laser deposition (PLD) and direct pulsed laser recrystallization (DPLR) are introduced to deposit superior transparent conductive oxide (TCO) layer on low melting point flexible substrates. As an indispensable component of thin film solar cell, TCO layer with a higher quality will improve the overall performance of solar cells. Alumina-doped zinc oxide (AZO), as one of the most promising TCO candidates, has now been widely used in solar cells. However, to achieve optimal electrical and optical properties of AZO on low melting point flexible substrate is challenging. Recently developed direct pulsed laser recrystallization (DPLR) technique is a scalable, economic and fast process for point defects elimination and recrystallization at room temperature. It features selective processing by only heating up the TCO thin film and preserve the underlying substrate at low temperature. In this study, 250 nm AZO thin film is pre-deposited by pulsed laser deposition (PLD) on flexible and rigid substrates. Then DPLR is introduced to achieve a uniform TCO layer on low melting point flexible substrates, i.e. commercialized Kapton polyimide film and micron-thick Al-foil. Both finite element analysis (FEA) simulation and designed experiments are carried out to demonstrate that DPLR is promising in manufacturing high quality AZO layers without any damage to the underlying flexible substrates. Under appropriate experiment conditions, such as 248 nm in laser wavelength, 25 ns in laser pulse duration, 15 laser pulses at laser fluence of 25 mJ/cm2, desired temperature would result in the AZO thin film and activate the grain growth and recrystallization. Besides laser conditions, the thermal conductivity and crystallinity of the substrate serve as additional factors in the DPLR process. It is found that the substrate's thermal conductivity correlates positively with the AZO crystal size; the substrate's crystallinity correlates positively with the AZO film's crystallinity. The thermal expansion of substrate would also contribute to the film tensile stress after processed by DPLR technique. The overall results indicate that DPLR technique is useful and scalable for flexible solar cell manufacturing.