In a manufacturing method of a semiconductor photonic device substrate, before multi-layer films different in material composition are successively and gradually crystal-grown in one chamber, an inter-layer growth rate model showing a relation in growth rate between each layer is defined, a growth rate of a film corresponding to at least one or more layers is obtained by actual crystal growth using an individual substrate, a growth rate of a film corresponding to other layers is estimated from the obtained growth rate by the inter-layer growth rate model, and a growth time is determined in accordance with a film thickness of each layer of the semiconductor photonic device substrate based on the actually obtained growth rate and the estimated growth rate. These steps are carried out by using a computer system connected to an MOCVD equipment, and then, a crystal growth of the semiconductor photonic device substrate is performed.