The present disclosure provides a color conversion substrate and manufacturing method thereof and a display panel. The color conversion substrate includes a base substrate; a color conversion layer on the base substrate and including a bank portion and a plurality of sub-portions having different colors, the bank portion is between adjacent sub-portions to separate the adjacent sub-portions and configured to absorb incident light, and the plurality of sub-portions having different colors are configured to convert the incident light in a same color into light having different colors; an anti-color-interference pattern on a side of the color conversion layer distal to the base substrate, an orthographic projection of the anti-color-interference pattern on the base substrate is within an orthographic projection of the bank portion on the base substrate, the anti-color-interference pattern is configured such that the incident light is refracted and then is transmitted into the bank portion.